-less for piping data
23 | # i.e: samtools view -h aligned_hits.bam | sam-less
24 | # Core syntaxes (default)
25 | alias clustal-less='source-highlight -f esc --lang-def=clustal.lang --outlang-def=bioSyntax.outlang --style-file=fasta.style | less'
26 | alias bed-less='source-highlight -f esc --lang-def=bed.lang --outlang-def=bioSyntax.outlang --style-file=sam.style | less'
27 | alias fa-less='source-highlight -f esc --lang-def=fasta.lang --outlang-def=bioSyntax.outlang --style-file=fasta.style | less'
28 | alias fq-less='source-highlight -f esc --lang-def=fastq.lang --outlang-def=bioSyntax.outlang --style-file=fasta.style | less'
29 | alias gtf-less='source-highlight -f esc --lang-def=gtf.lang --outlang-def=bioSyntax-vcf.outlang --style-file=vcf.style | less'
30 | alias pdb-less='source-highlight -f esc --lang-def=pdb.lang --outlang-def=bioSyntax-vcf.outlang --style-file=pdb.style | less'
31 | alias sam-less='source-highlight -f esc --lang-def=sam.lang --outlang-def=bioSyntax.outlang --style-file=sam.style | less'
32 | alias vcf-less='source-highlight -f esc --lang-def=vcf.lang --outlang-def=bioSyntax-vcf.outlang --style-file=vcf.style | less'
33 |
34 | # Auxillary syntaxes (uncomment to activate)
35 | #alias fai-less='source-highlight -f esc --lang-def=faidx.lang --outlang-def=bioSyntax.outlang --style-file=sam.style | less'
36 | #alias flagstat-less='source-highlight -f esc --lang-def=flagstat.lang --outlang-def=bioSyntax.outlang --style-file=sam.style | less'
37 |
--------------------------------------------------------------------------------
/docs/formats.md:
--------------------------------------------------------------------------------
1 | # File Format Compability in bioSyntax
2 |
3 | X = Syntax Complete
4 | O = Syntax Near-complete
5 | @ = Working Alpha
6 | ' ' = We're not there yet
7 | na = No planned development
8 |
9 | ## Core Syntaxes
10 |
11 | | File Format | Description | sublime | vim | gedit | less |
12 | |-------------|-----------------------------|:-------:|:---:|:-----:|:-----:|
13 | | .fasta | Generic nt/aa sequence | O | O | O | X |
14 | | .fq | Fasta + PHRED quality | X | O | @ | na |
15 | | .clustal | Multiple Sequence Alignment | X | | | na |
16 | | .bed | Genomic Ranges | O | | @ | na |
17 | | .gtf | Genomic Annotation | X | | | na |
18 | | .pdb | Protein Structure | X | | | na |
19 | | .vcf | Variant Call Format | O | | | X |
20 | | .sam | NGS Sequence Data | O | | O | X |
21 |
22 | ## Auxillary Syntaxes
23 |
24 | | File Format | Description | sublime | vim | gedit |
25 | |-------------|-----------------------------|:-------:|:---:|:-----:|
26 | | .faa | fasta with alt. aa colors) | | | |
27 | | - | Clustal | X | O | O |
28 | | - | Taylor | X | O | O |
29 | | - | Zappo | X | O | O |
30 | | - | Hydrophobicity | X | O | O |
31 | | .fai | Fasta Index | X | | |
32 | | .flagstat | samtools summary | X | | |
33 | | .wig | Wiggle data | O | | |
34 | | .newick | Tree Format | | | |
35 | | .phylip | Multiple Sequence Alignment | | | |
36 |
37 | Is your favorite file format not listed? Consider [collaborating](../collaborate.md) with us and adding it, we'll help you get started.
38 |
39 |
40 | [ under construction ]
41 | - Add links or better yet pop-up images for each file format to show examples on mouse-over
42 | -
--------------------------------------------------------------------------------
/syntax/sublime/bed.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Bed syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: bed
7 | file_extensions: [bed]
8 | scope: source.bed
9 |
10 |
11 | contexts:
12 | main:
13 | #Handle UCSC track line
14 | - match: '^track.*'
15 | scope: comment.bed
16 |
17 | # Column 1: Reference Sequence Name
18 | - match: '^[\S]*\t'
19 | scope: chr.bed
20 | push: start
21 |
22 | # Column 2: Start coordinate
23 | start:
24 | - match: ([0-9|\.]+)\b
25 | scope: chrStart.bed
26 | - match: \t
27 | push: end
28 | - match: $
29 | pop: true
30 |
31 | # Column 3: End Coordinate
32 | end:
33 | - match: ([0-9|\.]+)\b
34 | scope: chrEnd.bed
35 | - match: \t
36 | push: name
37 | - match: $
38 | pop: true
39 |
40 | # Column 4: Description / Name
41 | name:
42 | - match: '[\S]*'
43 | scope: string.bed
44 | - match: \t
45 | push: score
46 | - match: $
47 | pop: true
48 |
49 | # Column 5: Score (0-1000 scale)
50 | score:
51 | - match: \.\b
52 | scope: comment.bed
53 | - match: ([0-9])\b
54 | scope: grad1.bed
55 | - match: ([1-9][0-9])\b
56 | scope: grad1.bed
57 | - match: 1[0-9][0-9]\b
58 | scope: grad2.bed
59 | - match: 2[0-9][0-9]\b
60 | scope: grad3.bed
61 | - match: 3[0-9][0-9]\b
62 | scope: grad4.bed
63 | - match: 4[0-9][0-9]\b
64 | scope: grad5.bed
65 | - match: 5[0-9][0-9]\b
66 | scope: grad6.bed
67 | - match: 6[0-9][0-9]\b
68 | scope: grad7.bed
69 | - match: 7[0-9][0-9]\b
70 | scope: grad8.bed
71 | - match: 8[0-9][0-9]\b
72 | scope: grad9.bed
73 | - match: 9[0-9][0-9]\b
74 | scope: grad10.bed
75 | - match: ([0-9][0-9][0-9][0-9])\b
76 | scope: grad10.bed
77 | - match: \t
78 | push: strand
79 | - match: $
80 | pop: true
81 |
82 | # Column 6: Feature Strand
83 | strand:
84 | - match: \+
85 | scope: strandPlus.bed
86 | - match: \-
87 | scope: strandMinus.bed
88 | - match: \.
89 | scope: strandNone.bed
90 | - match: $
91 | pop: true
--------------------------------------------------------------------------------
/syntax/sublime/fastq.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Fastq syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: fastq
7 | file_extensions: [fastq, fq]
8 | scope: source.fastq
9 | # See http://www.sublimetext.com/docs/3/syntax.html
10 |
11 | contexts:
12 | main:
13 | # Lines which start with "@" are headers
14 | - match: "^@.*$"
15 | scope: header
16 | push: nt
17 |
18 | nt:
19 | # Nucleotide sequence highlighting
20 | - clear_scopes: true
21 | - match: "[Aa]+"
22 | scope: ntA
23 | - match: "[Gg]+"
24 | scope: ntG
25 | - match: "[Cc]+"
26 | scope: ntC
27 | - match: "[Tt]+"
28 | scope: ntT
29 | - match: "[Uu]+"
30 | scope: ntU
31 | - match: '^(?=\+)'
32 | set: commentLine
33 |
34 | commentLine:
35 | # Match the comment line "+"
36 | - clear_scopes: true
37 | - meta_scope: comment
38 | - match: "\n"
39 | set: quality
40 |
41 | quality:
42 | # Match PHRED-quality and graident-color
43 | - clear_scopes: true
44 | - match: "[\\!\\#\\$\"]"
45 | scope: gradbw0
46 | - match: "[%\\&\\'\\(]"
47 | scope: gradbw1
48 | - match: "[\\)\\*\\+\\,]"
49 | scope: gradbw2
50 | - match: "[\\-\\.\\/0]"
51 | scope: gradbw3
52 | - match: "[1-4]"
53 | scope: gradbw4
54 | - match: "[5-8]"
55 | scope: gradbw5
56 | - match: "[9\\:\\;\\<]"
57 | scope: gradbw6
58 | - match: "[\\=\\>\\?\\@]"
59 | scope: gradbw7
60 | - match: "[ABCD]"
61 | scope: gradbw8
62 | - match: "[EFGHIJ]"
63 | scope: gradbw9
64 | - match: "[K-Z\\[\\\\]"
65 | scope: gradbw10
66 | - match: "[\\]\\^\\_\\`a-f]"
67 | scope: gradbw10
68 | - match: "[g-p]"
69 | scope: gradbw10
70 | - match: "[q-z]"
71 | scope: gradbw10
72 | - match: "[\\{\\|\\}\\~]"
73 | scope: gradbw10
74 | - match: "\n"
75 | set: main
76 |
77 | # # Complete Phred Scale
78 | # #!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
79 | # #
80 | # # PHRED Scale - Illumina 1.8 Scale (Implemented)
81 | # # 0.2.......................26...31.......41 [Score]
82 | # # !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKL [ASCII]
83 | # # | | | | | | | | | | | ...
--------------------------------------------------------------------------------
/syntax/less/bioSyntax-vcf.outlang:
--------------------------------------------------------------------------------
1 | extension "bioSyntax"
2 | #version 0.1
3 | styletemplate "\x1b[$stylem$text\x1b[m"
4 | styleseparator ";"
5 |
6 | bold "01$style"
7 | underline "07$style"
8 | italics "03$style"
9 | color "$style"
10 |
11 | colormap
12 | # Nucleotide Colors
13 | "black" "30;48:5:253" # header
14 | "darkgreen" "30;48:5:10" # A
15 | "darkred" "30;48:5:09" # C, mal
16 | "darkblue" "30;48:5:33" # T, bon
17 | "brown" "30;48:5:214" # G
18 | "teal" "38:5:0;48:5:15" # N / REF
19 | #
20 | #
21 | # Text Class
22 | "gray" "38:5:240;48:5:255" # Comment
23 | "blue" "38:5:62" # Numeric, Version
24 | "yellow" "38:5:208" # Numeric2, Keyword4, software
25 | #
26 | #
27 | # Keyword
28 | "red" "38:5:160" # Keyword, string, quoteString
29 | "green" "38:5:28" # Keyword2, chr, chrStart
30 | "purple" "38:5:39" # Keyword3, url, library
31 | "cyan" "38:5:54" # Keyword5
32 | "pink" "38:5:136" # Keyword6
33 | "orange" "38:5:166" # Keyword7
34 | "brightgreen" "38:5:22" # Keyword8
35 | "brightorange" "38:5:18" # Keyword9
36 | default "30;"
37 | end
38 |
39 | ####################
40 | # Code color help
41 | #####################
42 |
43 | # 256 code color control template:
44 | # Code : \033[AA;FF;BBm
45 | # AA (attributes) : 00|01|03|04|05|07|22|23|24|25|27
46 | # FF (foreground) : 38;05;color
47 | # BB (background) : 48;05;color
48 | # color : 000-255
49 | # see: http://www.calmar.ws/vim/256-xterm-24bit-rgb-color-chart.html
50 | #
51 |
52 | # True-color (24 bit) - bioSyntax should be using 256-colors
53 | # FF (foreground) : 38:2:r:g:b
54 | # BB (background) : 48:2:r:g:b
55 |
56 | # Attributes meaning
57 | # 00 Reset
58 | # 01 Bold
59 | # 03 Italic
60 | # 04 Underline
61 | # 05 Blink (doesn't work when a background is set)
62 | # 07 Reverse (swap foreground and background)
63 | # 22 No Bold
64 | # 23 No Italic
65 | # 24 No Underline
66 | # 25 No Blink
67 | # 27 No Reverse
68 |
69 | # Any of AA,FF,BB may be omited.
70 | # Reset code (default color/attribute): \033[m
71 |
72 | # Examples:
73 | # -> Hello world in color 226 (=> yellow):
74 | # echo -e "\033[38;05;226mHello, World"
75 | # -> Hello world in bold blanking yellow:
76 | # echo -e "\033[01;05;38;05;226mHello, World"
77 | # -> Hello world in bold yellow with a red background:
78 | # echo -e "\033[01;38;05;226;48;05;196mHello, World"
79 |
--------------------------------------------------------------------------------
/syntax/less/bioSyntax.outlang:
--------------------------------------------------------------------------------
1 | extension "bioSyntax"
2 | # Version 0.1
3 | styletemplate "\x1b[$stylem$text\x1b[m"
4 | styleseparator ";"
5 |
6 | bold "01$style"
7 | underline "04$style"
8 | italics "03$style"
9 | color "$style"
10 |
11 | colormap
12 | # Nucleotide Colors
13 | "black" "30;48:5:253" # header
14 | "darkgreen" "30;48:5:10" # A
15 | "darkred" "30;48:5:09" # C
16 | "darkblue" "30;48:5:33" # G
17 | "brown" "30;48:5:214" # T
18 | "gray" "38:5:250" # NX, clip
19 |
20 | # Text Class
21 | "blue" "38:5:62" # Numeric
22 | "red" "38:5:160" # Keyword, string, mismatch
23 | "green" "38:5:28" # Keyword2, chr
24 | "purple" "38:5:39" # Keyword3, library, insertion
25 | "yellow" "38:5:166" # Keyword4, software, deletion
26 | "cyan" "38:5:54" # Keyword5,
27 |
28 | # BW Gradient coloring 5 step
29 | "teal" "38:5:243;48:5:0" # Gradient bw1
30 | "pink" "38:5:243;48:5:237" # Gradient bw3
31 | "orange" "38:5:237;48:5:243" # Gradient bw6
32 | "brightorange" "38:5:242;48:5:249" # Gradient bw8
33 | "brightgreen" "38:5:250;48:5:255" # Gradient bw10 +
34 | default "30;"
35 | end
36 |
37 | ####################
38 | # Code color help
39 | #####################
40 | #
41 | # 256 code color control template:
42 | # Code : \033[AA;FF;BBm
43 | # AA (attributes) : 00|01|03|04|05|07|22|23|24|25|27
44 | # FF (foreground) : 38;05;color
45 | # BB (background) : 48;05;color
46 | # color : 000-255
47 | # see: http://www.calmar.ws/vim/256-xterm-24bit-rgb-color-chart.html
48 | #
49 | #
50 | # True-color (24 bit) - bioSyntax should be using 256-colors
51 | # FF (foreground) : 38:2:r:g:b
52 | # BB (background) : 48:2:r:g:b
53 | #
54 | # Attributes meaning
55 | # 00 Reset
56 | # 01 Bold
57 | # 03 Italic
58 | # 04 Underline
59 | # 05 Blink (doesn't work when a background is set)
60 | # 07 Reverse (swap foreground and background)
61 | # 22 No Bold
62 | # 23 No Italic
63 | # 24 No Underline
64 | # 25 No Blink
65 | # 27 No Reverse
66 | #
67 | # Any of AA,FF,BB may be omited.
68 | # Reset code (default color/attribute): \033[m
69 | #
70 | # Examples:
71 | # -> Hello world in color 226 (=> yellow):
72 | # echo -e "\033[38;05;226mHello, World"
73 | # -> Hello world in bold blanking yellow:
74 | # echo -e "\033[01;05;38;05;226mHello, World"
75 | # -> Hello world in bold yellow with a red background:
76 | # echo -e "\033[01;38;05;226;48;05;196mHello, World"
77 |
--------------------------------------------------------------------------------
/docs/_site/index.md:
--------------------------------------------------------------------------------
1 | Syntax highlighting for computational biology in `vim`, `less`, `sublime3` & `gedit`.
2 |
3 | [A. Babaian](https://github.com/ababaian) \| [E. Chu](https://github.com/echu113) \| [A. Ebou](https://github.com/ebedthan) \| [A. Fegen](https://github.com/alyeffy) \| [J. Kam](https://github.com/lazypanda10117) \| [G. Novakovskiy](https://github.com/fransilvion) \| [J. Wong](https://github.com/Jwong684)
4 |
5 | [A hackseq17 project.](https://www.hackseq.com)
6 |
7 | ### [Watch the hackseq17 presentation (~5 min)](https://youtu.be/dHYN3E7edhY?t=6m28s)
8 |
9 | 
10 | 
11 |
12 | ## Installation (alphas)
13 |
14 | ### Sublime Text 3 Installation
15 |
16 | 1. Download the [bioMonokai Color Scheme](https://github.com/ababaian/bioSyntax/blob/master/dev/theme/sublime/Color%20Scheme%20-%20bioSyntax.sublime-package).
17 | 2. Copy it to your Sublime Text application packages folder:
18 | - **Linux**: `../sublime_text_3/Packages/`
19 | - **Windows**: `C:/Program Files/Sublime Text 3/Packages/`
20 | - **Mac**: `/Applications/Sublime Text.app/Contents/MacOS/Packages/`
21 | 3. Download the [bioSyntax sublime package](https://github.com/ababaian/bioSyntax/blob/master/syntax/bioSyntax_sublime_RELEASE.zip).
22 | 4. Unzip the `*.sublime-syntax` files into the Sublime Text Packages folder:
23 | - **Linux**: `~/.config/sublime-text-3/Packages/User/`
24 | - **Windows**: `%APPDATA%/Roaming/Sublime Text 3/Packages/`
25 | - **Mac**: `/Users/your_username/Library/Application Support/Sublime Text 3/Packages/`
26 | 5. Open Sublime Text and go select the bioSyntax (bioMonokai) theme
27 | `Preferences > Color Scheme > bioMonokai`
28 | 6. Formats should auto-detect; you can select a specific syntax at the drop-menu at the bottom-right corner of the window (e.g. Plain Text)
29 |
30 | You now have pretty formats!
31 |
32 | ### Gedit Installation (Linux)
33 | 1. Download the respective `*.lang` files you're interested in
34 | 2. Download the `bioKate.xml` style scheme
35 |
36 | 3. Change permissions to all readonly
37 | `chmod 0644 *.lang`
38 |
39 | 4. Copy the `bioKate.xml` style scheme to gtksoureview style folder
40 | `sudo cp bioKate.xml /usr/share/gtksourceview-3.0/styles/bioKate.xml`
41 |
42 | 5. Copy the `*.lang` file(s) to gtksourceview language spec folder
43 | `sudo cp fasta.lang /usr/share/gtksourceview-3.0/language-specs/fasta.lang`
44 |
45 | 6. Restart `gedit` and select the bioSyntax theme
46 | `Edit > Preferences > Font & Color > bioKate'`
47 | 7. You now have pretty formats
48 |
--------------------------------------------------------------------------------
/syntax/sublime/fasta-clustal.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Fasta-Clustal syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: fasta-clustal
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [fastaa,faa]
9 | scope: text.fasta-clustal
10 |
11 |
12 | contexts:
13 | main:
14 |
15 | #positive lookbehind to match a + and a new line to any characters right after it
16 | #pushes it to quality
17 | - match: "^>.*"
18 | scope: string
19 |
20 | # match amino acids
21 | # Alanine (ALA)
22 | - match: "[Aa]++"
23 | scope: aaA
24 |
25 | # Aspartate/Asparagine (ASX)
26 | - match: "[Bb]++"
27 | scope: aaB
28 |
29 | # Cysteine (CYS)
30 | - match: "[Cc]++"
31 | scope: aaC
32 |
33 | # Aspartate (ASP)
34 | - match: "[Dd]++"
35 | scope: aaD
36 |
37 | # Glutamate (GLU)
38 | - match: "[Ee]++"
39 | scope: aaE
40 |
41 | # Phenylalanine (PHE)
42 | - match: "[Ff]++"
43 | scope: aaF
44 |
45 | # Glycine (GLY)
46 | - match: "[Gg]++"
47 | scope: aaG
48 |
49 | # Histidine (HIS)
50 | - match: "[Hh]++"
51 | scope: aaH
52 |
53 | # Isoleucine (ILE)
54 | - match: "[Ii]++"
55 | scope: aaI
56 |
57 | # Lysine (LYS)
58 | - match: "[Kk]++"
59 | scope: aaK
60 |
61 | # Leucine (LEU)
62 | - match: "[Ll]++"
63 | scope: aaL
64 |
65 | # Methionine (MET)
66 | - match: "[Mm]++"
67 | scope: aaM
68 |
69 | # Asparagine (ASN)
70 | - match: "[Nn]++"
71 | scope: aaN
72 |
73 | # Proline (PRO)
74 | - match: "[Pp]++"
75 | scope: aaP
76 |
77 | # Glutamine (GLN)
78 | - match: "[Qq]++"
79 | scope: aaQ
80 |
81 | # Arginine (ARG)
82 | - match: "[Rr]++"
83 | scope: aaR
84 |
85 | # Serine (SER)
86 | - match: "[Ss]++"
87 | scope: aaS
88 |
89 | # Threonine (THE)
90 | - match: "[Tt]++"
91 | scope: aaT
92 |
93 | # Valine (VAL)
94 | - match: "[Vv]++"
95 | scope: aaV
96 |
97 | # Tryptophan (TRP)
98 | - match: "[Ww]++"
99 | scope: aaW
100 |
101 | # Tyrosine (TYR)
102 | - match: "[Yy]++"
103 | scope: aaY
104 |
105 | # Glutamate or Glutamine (GLX)
106 | - match: "[Zz]++"
107 | scope: aaZ
108 |
109 | # any/unknown (X)
110 | - match: "[Xx]++"
111 | scope: zappo.X
112 |
113 | # translation stop
114 | - match: "\\*"
115 | scope: comment
116 |
117 | # indel
118 | - match: "[-]++"
119 | scope: comment
120 |
--------------------------------------------------------------------------------
/syntax/sublime/fasta-zappo.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Fasta-Zappo syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: fasta-zappo
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [fastza]
9 | scope: text.fasta-zappoa
10 |
11 |
12 | contexts:
13 | main:
14 |
15 | #positive lookbehind to match a + and a new line to any characters right after it
16 | #pushes it to quality
17 | - match: "^>.*"
18 | scope: string
19 |
20 | # match amino acids
21 | # Alanine (ALA)
22 | - match: "[Aa]"
23 | scope: zappoA
24 |
25 | # Aspartate/Asparagine (ASX)
26 | - match: "[Bb]"
27 | scope: zappoB
28 |
29 | # Cysteine (CYS)
30 | - match: "[Cc]"
31 | scope: zappoC
32 |
33 | # Aspartate (ASP)
34 | - match: "[Dd]"
35 | scope: zappoD
36 |
37 | # Glutamate (GLU)
38 | - match: "[Ee]"
39 | scope: zappoE
40 |
41 | # Phenylalanine (PHE)
42 | - match: "[Ff]"
43 | scope: zappoF
44 |
45 | # Glycine (GLY)
46 | - match: "[Gg]"
47 | scope: zappoG
48 |
49 | # Histidine (HIS)
50 | - match: "[Hh]"
51 | scope: zappoH
52 |
53 | # Isoleucine (ILE)
54 | - match: "[Ii]"
55 | scope: zappoI
56 |
57 | # Lysine (LYS)
58 | - match: "[Kk]"
59 | scope: zappoK
60 |
61 | # Leucine (LEU)
62 | - match: "[Ll]"
63 | scope: zappoL
64 |
65 | # Methionine (MET)
66 | - match: "[Mm]"
67 | scope: zappoM
68 |
69 | # Asparagine (ASN)
70 | - match: "[Nn]"
71 | scope: zappoN
72 |
73 | # Proline (PRO)
74 | - match: "[Pp]"
75 | scope: zappoP
76 |
77 | # Glutamine (GLN)
78 | - match: "[Qq]"
79 | scope: zappoQ
80 |
81 | # Arginine (ARG)
82 | - match: "[Rr]"
83 | scope: zappoR
84 |
85 | # Serine (SER)
86 | - match: "[Ss]"
87 | scope: zappoS
88 |
89 | # Threonine (THE)
90 | - match: "[Tt]"
91 | scope: zappoT
92 |
93 | # Valine (VAL)
94 | - match: "[Vv]"
95 | scope: zappoV
96 |
97 | # Tryptophan (TRP)
98 | - match: "[Ww]"
99 | scope: zappoW
100 |
101 | # Tyrosine (TYR)
102 | - match: "[Yy]"
103 | scope: zappoY
104 |
105 | # Glutamate or Glutamine (GLX)
106 | - match: "[Zz]"
107 | scope: zappoZ
108 |
109 | # any/unknown (X)
110 | - match: "[Xx]"
111 | scope: zappoX
112 |
113 | # translation stop
114 | - match: "\\*"
115 | scope: comment
116 |
117 | # indel
118 | - match: "[-]"
119 | scope: comment
120 |
--------------------------------------------------------------------------------
/syntax/sublime/fasta-hydro.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Fasta-Hydrophobicity syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: fasta-hydro
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [fastahydro]
9 | scope: text.fasta-hydro
10 |
11 |
12 | contexts:
13 | main:
14 |
15 | #positive lookbehind to match a + and a new line to any characters right after it
16 | #pushes it to quality
17 | - match: "^>.*"
18 | scope: string
19 |
20 | # match amino acids
21 | # Alanine (ALA)
22 | - match: "[Aa]"
23 | scope: hydroA
24 |
25 | # Aspartate/Asparagine (ASX)
26 | - match: "[Bb]"
27 | scope: hydroB
28 |
29 | # Cysteine (CYS)
30 | - match: "[Cc]"
31 | scope: hydroC
32 |
33 | # Aspartate (ASP)
34 | - match: "[Dd]"
35 | scope: hydroD
36 |
37 | # Glutamate (GLU)
38 | - match: "[Ee]"
39 | scope: hydroE
40 |
41 | # Phenylalanine (PHE)
42 | - match: "[Ff]"
43 | scope: hydroF
44 |
45 | # Glycine (GLY)
46 | - match: "[Gg]"
47 | scope: hydroG
48 |
49 | # Histidine (HIS)
50 | - match: "[Hh]"
51 | scope: hydroH
52 |
53 | # Isoleucine (ILE)
54 | - match: "[Ii]"
55 | scope: hydroI
56 |
57 | # Lysine (LYS)
58 | - match: "[Kk]"
59 | scope: hydroK
60 |
61 | # Leucine (LEU)
62 | - match: "[Ll]"
63 | scope: hydroL
64 |
65 | # Methionine (MET)
66 | - match: "[Mm]"
67 | scope: hydroM
68 |
69 | # Asparagine (ASN)
70 | - match: "[Nn]"
71 | scope: hydroN
72 |
73 | # Proline (PRO)
74 | - match: "[Pp]"
75 | scope: hydroP
76 |
77 | # Glutamine (GLN)
78 | - match: "[Qq]"
79 | scope: hydroQ
80 |
81 | # Arginine (ARG)
82 | - match: "[Rr]"
83 | scope: hydroR
84 |
85 | # Serine (SER)
86 | - match: "[Ss]"
87 | scope: hydroS
88 |
89 | # Threonine (THE)
90 | - match: "[Tt]"
91 | scope: hydroT
92 |
93 | # Valine (VAL)
94 | - match: "[Vv]"
95 | scope: hydroV
96 |
97 | # Tryptophan (TRP)
98 | - match: "[Ww]"
99 | scope: hydroW
100 |
101 | # Tyrosine (TYR)
102 | - match: "[Yy]"
103 | scope: hydroY
104 |
105 | # Glutamate or Glutamine (GLX)
106 | - match: "[Zz]"
107 | scope: hydroZ
108 |
109 | # any/unknown (X)
110 | - match: "[Xx]"
111 | scope: hydroX
112 |
113 | # translation stop
114 | - match: "\\*"
115 | scope: comment
116 |
117 | # indel
118 | - match: "[-]"
119 | scope: comment
120 |
--------------------------------------------------------------------------------
/syntax/sublime/fasta-taylor.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Fasta-Taylor syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: fasta-taylor
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [fastaylor]
9 | scope: text.fasta-taylor
10 |
11 |
12 | contexts:
13 | main:
14 |
15 | #positive lookbehind to match a + and a new line to any characters right after it
16 | #pushes it to quality
17 | - match: "^>.*"
18 | scope: string
19 |
20 | # match amino acids
21 | # Alanine (ALA)
22 | - match: "[Aa]"
23 | scope: taylorA
24 |
25 | # Aspartate/Asparagine (ASX)
26 | - match: "[Bb]"
27 | scope: taylorB
28 |
29 | # Cysteine (CYS)
30 | - match: "[Cc]"
31 | scope: taylorC
32 |
33 | # Aspartate (ASP)
34 | - match: "[Dd]"
35 | scope: taylorD
36 |
37 | # Glutamate (GLU)
38 | - match: "[Ee]"
39 | scope: taylorE
40 |
41 | # Phenylalanine (PHE)
42 | - match: "[Ff]"
43 | scope: taylorF
44 |
45 | # Glycine (GLY)
46 | - match: "[Gg]"
47 | scope: taylorG
48 |
49 | # Histidine (HIS)
50 | - match: "[Hh]"
51 | scope: taylorH
52 |
53 | # Isoleucine (ILE)
54 | - match: "[Ii]"
55 | scope: taylorI
56 |
57 | # Lysine (LYS)
58 | - match: "[Kk]"
59 | scope: taylorK
60 |
61 | # Leucine (LEU)
62 | - match: "[Ll]"
63 | scope: taylorL
64 |
65 | # Methionine (MET)
66 | - match: "[Mm]"
67 | scope: taylorM
68 |
69 | # Asparagine (ASN)
70 | - match: "[Nn]"
71 | scope: taylorN
72 |
73 | # Proline (PRO)
74 | - match: "[Pp]"
75 | scope: taylorP
76 |
77 | # Glutamine (GLN)
78 | - match: "[Qq]"
79 | scope: taylorQ
80 |
81 | # Arginine (ARG)
82 | - match: "[Rr]"
83 | scope: taylorR
84 |
85 | # Serine (SER)
86 | - match: "[Ss]"
87 | scope: taylorS
88 |
89 | # Threonine (THE)
90 | - match: "[Tt]"
91 | scope: taylorT
92 |
93 | # Valine (VAL)
94 | - match: "[Vv]"
95 | scope: taylorV
96 |
97 | # Tryptophan (TRP)
98 | - match: "[Ww]"
99 | scope: taylorW
100 |
101 | # Tyrosine (TYR)
102 | - match: "[Yy]"
103 | scope: taylorY
104 |
105 | # Glutamate or Glutamine (GLX)
106 | - match: "[Zz]"
107 | scope: taylorZ
108 |
109 | # any/unknown (X)
110 | - match: "[Xx]"
111 | scope: taylorX
112 |
113 | # translation stop
114 | - match: "\\*"
115 | scope: comment
116 |
117 | # indel
118 | - match: "[-]"
119 | scope: comment
120 |
--------------------------------------------------------------------------------
/syntax/gedit/bed.lang:
--------------------------------------------------------------------------------
1 |
2 |
13 |
14 |
15 | text/bed
16 | *.bed
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 | ^\w+
36 |
37 |
38 |
39 |
40 |
41 | (?<=\t)[0-9]+\t[0-9]+(?=\t)
42 |
43 |
44 |
45 |
46 |
47 | (?<=\t)[A-Za-z()][^\s\t]+(?=\t)
48 |
49 |
50 |
51 |
52 |
53 | (?<=\t)[A-Za-z()][^\s\t]+$
54 |
55 |
56 |
57 |
58 |
59 | \t[+]\t
60 |
61 |
62 |
63 |
64 |
65 | \t[+]$
66 |
67 |
68 |
69 |
70 |
71 | \t[-]\t
72 |
73 |
74 |
75 |
76 |
77 | \t[-]$
78 |
79 |
80 |
81 |
82 |
83 | \t[.]\t
84 |
85 |
86 |
87 |
88 |
89 | \t[.]$
90 |
91 |
92 |
93 |
94 |
95 |
96 |
97 |
--------------------------------------------------------------------------------
/syntax/sublime/wig.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Wig syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: wig
7 | file_extensions: [wig]
8 | scope: source.wig
9 |
10 | contexts:
11 | main:
12 | #find declaration line
13 | #declared as fixedStep
14 | - match: fixedStep\s
15 | scope: chr.wig
16 | push: fchrom
17 |
18 | #declared as varibleStep
19 | - match: variableStep\s
20 | scope: keyword.wig
21 | push: vchrom
22 |
23 | #color data value for variableStep format
24 | - match: (?=([0-9]+\s\d+\s))([0-9]+\s)
25 | scope: numeric.wig
26 | push: colorData
27 |
28 | #color data value for fixedStep format
29 | - match: (?=\d+\s)
30 | scope: numeric.wig
31 | push: colorData
32 |
33 | #fixedStep chromosome name
34 | fchrom:
35 | - match: chrom
36 | scope: chr.wig
37 | - match: \=
38 | scope: comment.wig
39 | - match: \s
40 | push: fstart
41 | - match: $
42 | pop: true
43 |
44 | #fixedStep start position
45 | fstart:
46 | - match: start
47 | scope: chrStart.wig
48 | - match: \s
49 | push: fstep
50 | - match: $
51 | pop: true
52 |
53 | #fixedStep step interval
54 | fstep:
55 | - match: step
56 | scope: numeric.wig
57 | - match: $
58 | pop: true
59 |
60 | #variableStep chromosome name
61 | vchrom:
62 | - match: chrom
63 | scope: chr.wig
64 | - match: \s
65 | push: vspan
66 | - match: $
67 | pop: true
68 |
69 | #variableStep span
70 | vspan:
71 | - match: span
72 | scope: numeric.wig
73 | - match: $
74 | pop: true
75 |
76 | #data values will be passed to here and be painted
77 | colorData:
78 | - match: \.\b
79 | scope: comment.gtf
80 | - match: ([1-9]|[1-9].\d+)\b
81 | scope: grad1.gtf
82 | - match: ([1-9])([0-9]|[0-9].\d+)\b
83 | scope: grad1.gtf
84 | - match: 1([0-9]{2}|[0-9]{2}.\d+)\b
85 | scope: grad2.gtf
86 | - match: 2([0-9]{2}|[0-9]{2}.\d+)\b
87 | scope: grad3.gtf
88 | - match: 3([0-9]{2}|[0-9]{2}.\d+)\b
89 | scope: grad4.gtf
90 | - match: 4([0-9]{2}|[0-9]{2}.\d+)\b
91 | scope: grad5.gtf
92 | - match: 5([0-9]{2}|[0-9]{2}.\d+)\b
93 | scope: grad6.gtf
94 | - match: 6([0-9]{2}|[0-9]{2}.\d+)\b
95 | scope: grad7.gtf
96 | - match: 7([0-9]{2}|[0-9]{2}.\d+)\b
97 | scope: grad8.gtf
98 | - match: 8([0-9]{2}|[0-9]{2}.\d+)\b
99 | scope: grad9.gtf
100 | - match: 9([0-9]{2}|[0-9]{2}.\d+)\b
101 | scope: grad10.gtf
102 | - match: ([1-9])([0-9]{2,}|[0-9]{2,}.\d+)\b
103 | scope: grad10.gtf
104 | - match: $
105 | pop: true
--------------------------------------------------------------------------------
/docs/_layouts/default.html:
--------------------------------------------------------------------------------
1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
9 |
10 |
11 |
12 | {% seo %}
13 |
14 |
15 |
16 |
17 |
18 |
34 |
35 |
36 |
37 |
40 |
41 |
42 |
43 |
52 |
53 | {% if site.google_analytics %}
54 |
62 | {% endif %}
63 |
64 |
65 |
--------------------------------------------------------------------------------
/syntax/less/pdb.lang:
--------------------------------------------------------------------------------
1 | # VCF language definition file for less pipe
2 | # bioSyntax v0.1
3 | # Depends on vcf.style + bioSyntax-vcf.outlang
4 |
5 | # Variables ----------------------------------
6 | vardef NUCLEOTIDE = '[ATCGNXatcgnxRYSWKMBVDH]'
7 | vardef PHRED = '[!-K]' #PHRED 1.8
8 |
9 | vardef NUMERICTAG = '(Number=|Type=|Date=|Version=)'
10 | vardef QUOTETAG = '(Description=)'
11 | vardef STRINGTAG = '(\w+=)' # all others
12 |
13 | # Header Area -------------------------------
14 |
15 | # Header
16 | header start '^HEADER'
17 |
18 | # Title
19 | keyword5 start '^TITLE'
20 |
21 | # Compoud
22 | string start '^COMPND'
23 |
24 | # Source
25 | keyword5 start '^SOURCE'
26 |
27 | # Keywords
28 | keyword start '^KEYWDS'
29 |
30 | # Experiment Type
31 | keyword start '^EXPDTA'
32 |
33 | # Authors
34 | keyword start '^AUTHOR'
35 |
36 | # Revision Date
37 | keyword start '^REVDAT'
38 |
39 | # Publication
40 | state keyword6 start '^JRNL' begin
41 | endline = '$' exit
42 | # Authors
43 | keyword4 start '\bTITL'
44 | # Else
45 | keyword6 start '\b\S'
46 |
47 | end
48 |
49 | # Remarks
50 | state keyword5 start '^REMARK' begin
51 | endline = '$' exit
52 |
53 | # Null in variable
54 | string = 'NULL'
55 |
56 | state variable_data start ':' begin
57 | endline = '$' exit
58 |
59 | # Null in variable
60 | string = 'NULL'
61 |
62 | # Variable Numeric Data
63 | keyword = '[\d\.e\-]++'
64 |
65 | # Variable string Data
66 | keyword = '[^;]'
67 |
68 | end
69 | # Remark Variables
70 | keyword6 = 'RESOLUTION'
71 |
72 | # Other Remark text
73 | keyword5 = '[^:;]'
74 | end
75 |
76 | # Chain AA-Sequence Data
77 | state keyword5 start '^SEQRES' begin
78 | endline = '$' exit
79 |
80 | keyword start '[\s\t]+[0-9]+[\s\t]+[AGMSY]'
81 | keyword2 start '[\s\t]+[0-9]+[\s\t]+[BHNTZ]'
82 | keyword3 start '[\s\t]+[0-9]+[\s\t]+[CIOU]'
83 | keyword4 start '[\s\t]+[0-9]+[\s\t]+[DJPV]'
84 | keyword5 start '[\s\t]+[0-9]+[\s\t]+[EKQW]'
85 | keyword6 start '[\s\t]+[0-9]+[\s\t]+[FLRX]'
86 |
87 | end
88 |
89 | # Secondary Structure
90 | keyword start '^HELIX'
91 | string start '^SHEET'
92 | keyword start '^SITE'
93 |
94 | # Atomic Data
95 | state keyword5 start '^(ATOM|ANISOU)' begin
96 | endline = '$' exit
97 |
98 | keyword5 = '\A[\s]+[0-9]++[\s]++[\S]{0,3}\s'
99 |
100 | # Amino Acid Coloring CLUSTAL hardcode
101 | aaHydro = '\s+(ALA|ILE|LEU|MET|PHE|TRP|VAL)'
102 | aaPos = '\s+(LYS|ARG)'
103 | aaNeg = '\s+(GLU|ASP)'
104 | aaPol = '\s+(ASN|GLN|SER|THR)'
105 | aaCys = '\s+CYS'
106 | aaGly = '\s+GLY'
107 | aaAro = '\s+(TYR|HIS)'
108 |
109 | # Apply inverse coloring of Chain colors above
110 | keydrow = '(?<=\s)[AGMSY](?=\s)'
111 | keydrow2 = '(?<=\s)[BHNTZ](?=\s)'
112 | keydrow3 = '(?<=\s)[CIOU](?=\s)'
113 | keydrow4 = '(?<=\s)[DJPV](?=\s)'
114 | keydrow5 = '(?<=\s)[EKQW](?=\s)'
115 | keydrow6 = '(?<=\s)[FLRX](?=\s)'
116 |
117 | state keyword ='\d+\s' begin
118 | endline = '$' exit
119 |
120 | keyword5 start '.'
121 |
122 | end
123 | end
124 |
--------------------------------------------------------------------------------
/syntax/sublime/gtf.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Flagstat syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: gtf
7 | file_extensions: [gtf]
8 | scope: source.gtf
9 | # Specification: http://mblab.wustl.edu/GTF22.html
10 |
11 | contexts:
12 | main:
13 | - match: '^[\S]*\t'
14 | scope: chr.gtf
15 | push: source
16 |
17 | source:
18 | - match: '[\S]*'
19 | scope: variable.parameter.gtf
20 | - match: \t
21 | push: feature
22 | - match: $
23 | pop: true
24 |
25 | feature:
26 | - match: 'exon'
27 | scope: exonLevel.gtf
28 | - match: 'transcript'
29 | scope: transcriptLevel.gtf
30 | - match: 'CDS'
31 | scope: cds.gtf
32 | - match: 'start_codon'
33 | scope: start_codon.gtf
34 | - match: 'stop_codon'
35 | scope: stop_codon.gtf
36 | - match: \t
37 | push: start
38 | - match: $
39 | pop: true
40 |
41 | start:
42 | - match: ([0-9|\.]+)\b
43 | scope: chrStart.gtf
44 | - match: \t
45 | push: end
46 | - match: $
47 | pop: true
48 |
49 | end:
50 | - match: ([0-9|\.]+)\b
51 | scope: chrEnd.gtf
52 | - match: \t
53 | push: score
54 | - match: $
55 | pop: true
56 |
57 | score:
58 | - match: \.\b
59 | scope: comment.gtf
60 | - match: ([1-9])\b
61 | scope: grad1.gtf
62 | - match: ([1-9][0-9])\b
63 | scope: grad1.gtf
64 | - match: 1[0-9][0-9]\b
65 | scope: grad2.gtf
66 | - match: 2[0-9][0-9]\b
67 | scope: grad3.gtf
68 | - match: 3[0-9][0-9]\b
69 | scope: grad4.gtf
70 | - match: 4[0-9][0-9]\b
71 | scope: grad5.gtf
72 | - match: 5[0-9][0-9]\b
73 | scope: grad6.gtf
74 | - match: 6[0-9][0-9]\b
75 | scope: grad7.gtf
76 | - match: 7[0-9][0-9]\b
77 | scope: grad8.gtf
78 | - match: 8[0-9][0-9]\b
79 | scope: grad9.gtf
80 | - match: 9[0-9][0-9]\b
81 | scope: grad10.gtf
82 | - match: ([0-9][0-9][0-9][0-9])\b
83 | scope: grad10.gtf
84 | - match: \t
85 | push: strand
86 | - match: $
87 | pop: true
88 |
89 | strand:
90 | - match: \+
91 | scope: strandPlus.gtf
92 | - match: \-
93 | scope: strandMinus.gtf
94 | - match: \.
95 | scope: strandNone.gtf
96 | - match: \t
97 | push: frame
98 | - match: $
99 | pop: true
100 |
101 | frame:
102 | - match: ([0-2])\b
103 | scope: numeric.gtf
104 | - match: \.
105 | scope: comment.gtf
106 | - match: \t
107 | push: attribute
108 | - match: $
109 | pop: true
110 |
111 | attribute:
112 | - match: \b[^\s;]+(?=\s"[\w|\W|\_|\.]*")
113 | scope: gradbw5.attributeName.gtf
114 | - match: (?="[\w|\d|\.]+";)"[\d|\.]+"
115 | scope: numeric.attributeNumbers.gtf
116 | - match: (?="[\w|\d|\.|\-|\_|\:]+";)"[\w|\d|\.|\-|\_|\:]+"
117 | scope: grad4.attributeString.gtf
118 | - match: \b[^\s;]+(?=\s[\w|\W|\_|\.])
119 | scope: gradbw5.attributeName.gtf
120 | - match: (?=\d+;)\d+
121 | scope: numeric.attributeNumbers.gtf
122 | - match: \t
123 | push: attribute
124 | - match: $
125 | pop: true
126 |
127 |
--------------------------------------------------------------------------------
/syntax/less/gtf.lang:
--------------------------------------------------------------------------------
1 | # GTF language definition file for less pipe
2 | # bioSyntax v0.1
3 | # Depends on vcf.style + bioSyntax-vcf.outlang
4 |
5 | # Comment or UCSC Track information
6 | # is lines beginning with "#""
7 | comment start "#"
8 |
9 |
10 | # GTF Data
11 | # Column 1: chr or seqname
12 | environment push1 start '^(?=[A-Za-z])' begin
13 | drop = '$' exitall # stops multi-line searching
14 | chr = '^\S++'
15 |
16 | # Column 2: source of annotation
17 | environment push2 = '\t?' begin
18 | drop = '(?=$)' exitall
19 | software = '\A\S++'
20 |
21 | # Column 3: feature type
22 | environment push3 = '\t?' begin
23 | drop = '(?=$)' exitall
24 | # GTF Specification Types
25 | ## CDS, start_codon, stop_codon
26 | ## 5UTR, 3UTR, inter, inter_CNS, intron_CNS, exon
27 | # Other used types (non-specification)
28 | # gene, transcript
29 |
30 | keyword2b = 'gene'
31 | keyword2i = 'transcript'
32 | keyword5 = 'exon'
33 |
34 | nob = 'CDS'
35 | bon = 'start_codon'
36 | mal = 'stop_codon'
37 | comment = '[35]?UTR'
38 | comment = 'inter'
39 | comment = 'inter_CNS'
40 | comment = 'intron_CNS'
41 |
42 | comment = '\A\S+' # Non-standard Catch-all
43 |
44 | # Column 4: chr Start
45 | environment push4 = '\t?' begin
46 | drop = '(?=$)' exitall
47 | chrStart = '\A\d+'
48 |
49 | # Column 5: chr End
50 | environment push5 = '\t?' begin
51 | drop = '(?=$)' exitall
52 | chrStart = '\A\d+'
53 |
54 | # Column 6: Feature Score (0-1000)
55 | environment push6 = '\t?' begin
56 | drop = '(?=$)' exitall
57 | numeric = '\A[.\d]+'
58 |
59 | # Column 7: Feature Strand
60 | environment push7 = '\t?' begin
61 | drop = '(?=$)' exitall
62 | ntT = '\A\+'
63 | ntG = '\A\-'
64 | ntN = '\A\S'
65 |
66 | # Column 8: Feature Frame (.,0,1,2)
67 | # TODO: possibly add strand-detection here
68 | # and merge column 7+8
69 | environment push8 = '\t?' begin
70 | drop = '(?=$)' exitall
71 | keyword6 = '\A\.'
72 | keyword6 = '\A0'
73 | keyword4 = '\A1'
74 | keyword = '\A2'
75 |
76 | # Column 9: Attributes
77 | environment push9 = '\t?' begin
78 | drop = '(?=$)' exitall
79 |
80 | # gene_id / transcript_id special
81 | environment push10 = '(gene_id |transcript_id |gene_name )' begin
82 | drop = '(?=$)' exitall
83 | drop = '(?=;)' exit
84 | keywordi2 delim "\"" "\""
85 | end
86 |
87 | # Generic Numeric
88 | numeric = '"[\d\.e]++"' #quoted
89 | numeric = '\b\d++;' #unquoted
90 |
91 | # Generic String Quoted
92 | quoteString = '"\S+"'
93 |
94 | end #col8
95 | end #col8
96 | end #col7
97 | end #col6
98 | end # col5
99 | end # col4
100 | end # col3
101 | end # col2
102 | end # bed data section
103 |
--------------------------------------------------------------------------------
/examples/nt-seq/test_alignment1.phylip:
--------------------------------------------------------------------------------
1 | 30 112
2 | CryptosporAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUCCGUAGUCUUAACCAUAAA
3 | Yarrowia_lAAGAACGAAAGUUAGGGGAUCAAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCGUAAA
4 | ThalassiosAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUAC.CAUC.GUAGUCUUAACCAUAAA
5 | GuillardiaAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAA
6 | Aedes_alboAAGAACGAAAGUUAGAGGAUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUAACCGUAAA
7 | CyanidioscAAGAACGAAAGUUAGGGGAUCGAAGACGAUUAGAUAC.CGUC.GUAGUCUUAACCAUAAA
8 | TetrahymenAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACUAUAAA
9 | DictyostelAAGAACGAAAGUUUGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCCAAACUAUAAA
10 | PlasmodiumAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUAC.CGUC.GUAAUCUUAACCAUAAA
11 | SchizosaccAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAA
12 | CaenorhabdAAGAACGAAAGUCAGAGGUUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUGACCGUAAA
13 | LeishmaniaAAGAACCAAAGUGUGGAGAUCGAAGAUGAUUAGAGAC.CAUU.GUAGUCCACACUGCAAA
14 | CaenorhabdAAGAACGAAAGUCAGAGGUUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUGACCGUAAA
15 | SaccharomyAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAA
16 | Xenopus_laAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
17 | EremotheciAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAA
18 | TrypanosomAAGAACCAAAGUGUGGGGAUCAAAGAUGAUUAGAGAC.CAUU.GUAGUCCACACUGCAAA
19 | Latimeria AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
20 | Adineta_vaAAGAACGAAAGUUUGAGGUUCGAAGACGAUUAGAUAC.CGUC.CUAGUUCAAACCAUAAA
21 | Danio_reriAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCGUAAA
22 | Anolis_carAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
23 | Gallus_galAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
24 | Oryza_satiAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUAC.CGUC.CUAGUCUCAACCAUAAA
25 | ArabidopsiAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUAC.CGUC.CUAGUCUCAACCAUAAA
26 | Homo_sapieAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
27 | Rattus_norAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
28 | MonodelphiAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACUCGUC.GUAGUUCCGACCAUAAA
29 | Mus_musculAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
30 | DrosophilaAAGAACGAAAGUUAGAGGUUCGAAGGCGAUCAGAUAC.CGCC.CUAGUUCUAACCAUAAA
31 | Pan_trogloAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUG.GUAGUUCUGUCCAUAAA
32 |
33 | CUAUGC.CAACU.AGAGAUUGGAGGU.UGU.U....................
34 | CUAUGC.CGACU.GAGAAUGGGUA.C.CG.......................
35 | CUAUGC.CGACU.CGGGAUUGGCGGU.UGU.U....................
36 | CUAUGC.CGACU.AGGGAUCAGUGGA.UGU.C....................
37 | CUAUGC.CAAUU.AGCAAUUGGGAGA.CGC.U....................
38 | CGAUGC.CGACU.CGGGAUCGGUGGAG.CA.C....................
39 | CUAUAC.CGACU.CGGGAUCGGCUGG..A.......................
40 | CUAUGU.CGACC.AGGGAUCGGUUAA.AAU.U....................
41 | CUAUGC.CGACU.AGGUGUUGGAUGA.AAG.UGUUAAAAAUAAAAGUCAUCU
42 | CUAUGC.CGACU.AGGGAUCGGGCAA.UGU.U....................
43 | CGAUGC.CAUCU.CGCGAUUCGGAGG..G..U....................
44 | CGAUGA.CACCC.AUGAAUUGGGGAU.CUU.AUG......GG..........
45 | CGAUGC.CAUCU.CGCGAUUCGGAGG..G..U....................
46 | CUAUGC.CGACU.AGGGAUCGGGUGG.UGU.U....................
47 | CGAUGC.CGACU.AGCGAUCCGGCGG.CGU.U....................
48 | CUAUGC.CGACU.AGGGAUCGGGUGG.UGU.U....................
49 | CCAUGA.CACCC.AUGAAUUGGGGAACAUCAUUG......GG..........
50 | CGAUGC.CAACU.ACCGAUCCGGCGG.CGU.U....................
51 | CGUUGC.CAACU.GUCUUUUAGAUGC.GGU.U....................
52 | CGAUGC.CGACC.CGCGAUCCGGCGG.CGU.U....................
53 | CGAUGC.CGACU.AGCGAUCCGGCGG.CGU.U....................
54 | CGAUGC.CGACU.CGCGAUCCGGCGG.CGU.U....................
55 | CGAUGC.CGACC.AGGGAUCGGCGGA.UGU.U....................
56 | CGAUGC.CGACC.AGGGAUCAGCGGA.UGU.U....................
57 | CGAUGC.CGACC.GGCGAUGCGGCGG.CGU.U....................
58 | CGAUGC.CGACU.GGCGAUGCGGCGG.CGU.U....................
59 | CGAUGCUCGACU.AGCGAUCCGGCGG.CGU.U....................
60 | CGAUGC.CGACU.GGCGAUGCGGCGG.CGU.U....................
61 | CGAUGC.CAGCU.AGCAAUUGGGUGU.AGC.U....................
62 | CGAAGC.CGACU.GGCAACGUGGCGG.UGU.U....................
63 |
--------------------------------------------------------------------------------
/docs/_sass/rouge-github.scss:
--------------------------------------------------------------------------------
1 | .highlight table td { padding: 5px; }
2 | .highlight table pre { margin: 0; }
3 | .highlight .cm {
4 | color: #777772;
5 | font-style: italic;
6 | }
7 | .highlight .cp {
8 | color: #797676;
9 | font-weight: bold;
10 | }
11 | .highlight .c1 {
12 | color: #777772;
13 | font-style: italic;
14 | }
15 | .highlight .cs {
16 | color: #797676;
17 | font-weight: bold;
18 | font-style: italic;
19 | }
20 | .highlight .c, .highlight .cd {
21 | color: #777772;
22 | font-style: italic;
23 | }
24 | .highlight .err {
25 | color: #a61717;
26 | background-color: #e3d2d2;
27 | }
28 | .highlight .gd {
29 | color: #000000;
30 | background-color: #ffdddd;
31 | }
32 | .highlight .ge {
33 | color: #000000;
34 | font-style: italic;
35 | }
36 | .highlight .gr {
37 | color: #aa0000;
38 | }
39 | .highlight .gh {
40 | color: #797676;
41 | }
42 | .highlight .gi {
43 | color: #000000;
44 | background-color: #ddffdd;
45 | }
46 | .highlight .go {
47 | color: #888888;
48 | }
49 | .highlight .gp {
50 | color: #555555;
51 | }
52 | .highlight .gs {
53 | font-weight: bold;
54 | }
55 | .highlight .gu {
56 | color: #aaaaaa;
57 | }
58 | .highlight .gt {
59 | color: #aa0000;
60 | }
61 | .highlight .kc {
62 | color: #000000;
63 | font-weight: bold;
64 | }
65 | .highlight .kd {
66 | color: #000000;
67 | font-weight: bold;
68 | }
69 | .highlight .kn {
70 | color: #000000;
71 | font-weight: bold;
72 | }
73 | .highlight .kp {
74 | color: #000000;
75 | font-weight: bold;
76 | }
77 | .highlight .kr {
78 | color: #000000;
79 | font-weight: bold;
80 | }
81 | .highlight .kt {
82 | color: #445588;
83 | font-weight: bold;
84 | }
85 | .highlight .k, .highlight .kv {
86 | color: #000000;
87 | font-weight: bold;
88 | }
89 | .highlight .mf {
90 | color: #009999;
91 | }
92 | .highlight .mh {
93 | color: #009999;
94 | }
95 | .highlight .il {
96 | color: #009999;
97 | }
98 | .highlight .mi {
99 | color: #009999;
100 | }
101 | .highlight .mo {
102 | color: #009999;
103 | }
104 | .highlight .m, .highlight .mb, .highlight .mx {
105 | color: #009999;
106 | }
107 | .highlight .sb {
108 | color: #d14;
109 | }
110 | .highlight .sc {
111 | color: #d14;
112 | }
113 | .highlight .sd {
114 | color: #d14;
115 | }
116 | .highlight .s2 {
117 | color: #d14;
118 | }
119 | .highlight .se {
120 | color: #d14;
121 | }
122 | .highlight .sh {
123 | color: #d14;
124 | }
125 | .highlight .si {
126 | color: #d14;
127 | }
128 | .highlight .sx {
129 | color: #d14;
130 | }
131 | .highlight .sr {
132 | color: #009926;
133 | }
134 | .highlight .s1 {
135 | color: #d14;
136 | }
137 | .highlight .ss {
138 | color: #990073;
139 | }
140 | .highlight .s {
141 | color: #d14;
142 | }
143 | .highlight .na {
144 | color: #008080;
145 | }
146 | .highlight .bp {
147 | color: #797676;
148 | }
149 | .highlight .nb {
150 | color: #0086B3;
151 | }
152 | .highlight .nc {
153 | color: #445588;
154 | font-weight: bold;
155 | }
156 | .highlight .no {
157 | color: #008080;
158 | }
159 | .highlight .nd {
160 | color: #3c5d5d;
161 | font-weight: bold;
162 | }
163 | .highlight .ni {
164 | color: #800080;
165 | }
166 | .highlight .ne {
167 | color: #990000;
168 | font-weight: bold;
169 | }
170 | .highlight .nf {
171 | color: #990000;
172 | font-weight: bold;
173 | }
174 | .highlight .nl {
175 | color: #990000;
176 | font-weight: bold;
177 | }
178 | .highlight .nn {
179 | color: #555555;
180 | }
181 | .highlight .nt {
182 | color: #000080;
183 | }
184 | .highlight .vc {
185 | color: #008080;
186 | }
187 | .highlight .vg {
188 | color: #008080;
189 | }
190 | .highlight .vi {
191 | color: #008080;
192 | }
193 | .highlight .nv {
194 | color: #008080;
195 | }
196 | .highlight .ow {
197 | color: #000000;
198 | font-weight: bold;
199 | }
200 | .highlight .o {
201 | color: #000000;
202 | font-weight: bold;
203 | }
204 | .highlight .w {
205 | color: #bbbbbb;
206 | }
207 | .highlight {
208 | background-color: #f8f8f8;
209 | }
210 |
--------------------------------------------------------------------------------
/syntax/gedit/fastq.lang:
--------------------------------------------------------------------------------
1 |
2 |
11 |
12 |
13 | text/fasta
14 | *.fq;*.fastq
15 |
16 |
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
48 |
49 |
50 |
51 | [Aa]+
52 |
53 |
54 | [Tt]+
55 |
56 |
57 | [Gg]+
58 |
59 |
60 | [Cc]+
61 |
62 |
63 |
64 |
120 |
121 |
122 |
123 |
124 |
--------------------------------------------------------------------------------
/syntax/gedit/clustal.lang:
--------------------------------------------------------------------------------
1 |
2 |
13 |
14 |
15 | text/clustal
16 | *.clustal
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
51 |
52 |
53 | \S++(?=\s)
54 |
55 |
56 |
57 |
58 | [Aa]++
59 |
60 |
61 | [Tt]++
62 |
63 |
64 | [Gg]++
65 |
66 |
67 | [Cc]++
68 |
69 |
70 | [Uu]++
71 |
72 |
73 | [XxNn]++
74 |
75 |
76 | [\-\.]++
77 |
78 |
79 |
80 |
81 | [Rr]++
82 |
83 |
84 | [Yy]++
85 |
86 |
87 | [Ss]++
88 |
89 |
90 | [Ww]++
91 |
92 |
93 | [Mm]++
94 |
95 |
96 | [Kk]++
97 |
98 |
99 | [Dd]++
100 |
101 |
102 | [Bb]++
103 |
104 |
105 | [Vv]++
106 |
107 |
108 | [Hh]++
109 |
110 |
111 |
112 |
113 |
114 |
115 |
--------------------------------------------------------------------------------
/syntax/vim/gtf.vim:
--------------------------------------------------------------------------------
1 | if exists("syntax_on")
2 | syntax reset
3 | colorscheme bioSyntax
4 | set nowrap
5 | endif
6 |
7 | " Robust Column Selection in Vim Syntax
8 | " " -- This logic can be extended for N columns
9 | " " -- To add highlighting to a column add it to the contains list (submatch)
10 | syntax region Col1 matchgroup=Col1 start='^' end='\n' contains=Col2
11 | syntax region Col2 matchgroup=Col2 start='\t' end='\n\@=' contains=Col3
12 | syntax region Col3 matchgroup=Col3 start='\t' end='\n\@=' contains=Col4,s,s2,s3,s4,s5,s6,s7,s8,s9
13 | syntax region Col4 matchgroup=Col4 start='\t' end='\n\@=' contains=Col5
14 | syntax region Col5 matchgroup=Col5 start='\t' end='\n\@=' contains=Col6
15 | syntax region Col6 matchgroup=Col6 start='\t' end='\n\@=' contains=Col7
16 | syntax region Col7 matchgroup=Col7 start='\t' end='\n\@=' contains=Col8,plus,minus
17 | syntax region Col8 matchgroup=Col8 start='\t' end='\n\@=' contains=Col9,zero,one,two
18 | syntax region Col9 matchgroup=Col9 start='\t' end='\n\@=' contains=strg,num,gene_type,semi,id,geneName,havana,ont
19 |
20 | " " -- To create a region just for strings inside Col9
21 | syntax region strg matchgroup=strg start='\s"\@=' end=';' contains=na,num2
22 | syntax region id matchgroup=id start='\(\(gene_id\|transcript_id\|exon_id\|protein_id\)\s"\)\@=' end=';' contains=ens
23 | syntax region geneName matchgroup=geneName start='\(\(gene_name\|transcript_name\)\s"\)\@=' end=';' contains=gene_name
24 | syntax region ont matchgroup=ont start='\(\(ont\)\s"\)\@=' end=';' contains=ont_name
25 | syntax region havana matchgroup=havana start='\(\(havana_gene\|havana_transcript\)\s"\)\@=' end=';' contains=havName
26 |
27 |
28 | " " -- To identify the header #
29 | syntax region header matchgroup=header start='#' end='\n\@='
30 | "
31 | " " Submatch Definitions
32 | " " specific colours under type
33 | syntax match s 'exon' contained
34 | syntax match s2 'transcript' contained
35 | syntax match s3 'gene' contained
36 | syntax match s4 'start_codon' contained
37 | syntax match s5 'stop_codon' contained
38 | syntax match s6 'CDS' contained
39 | syntax match s7 '5UTR' contained
40 | syntax match s8 '3UTR' contained
41 | syntax match s9 'UTR' contained
42 |
43 | " " specific colours for strand
44 | syntax match plus '+' contained
45 | syntax match minus '-' contained
46 |
47 | " " matches within Col8
48 | syntax match zero '0' contained
49 | syntax match one '1' contained
50 | syntax match two '2' contained
51 |
52 |
53 | " " matches within Col9 (i.e. non-string - in general)
54 | syntax match num '\d' contained
55 | syntax match semi ';' contained
56 |
57 | " " matches within strings
58 | " syntax match ident '"\<\w*_\w*\>"' contained
59 | syntax match ens '"\<[0-9A-Za-z.-_]*\>"' contained
60 | " " matches NA
61 | syntax match na '"NA"' contained
62 | " " matches numerics in strings
63 | syntax match num2 '"[-+][0-9]\+\.\d*"' contained
64 | syntax match num2 '"[0-9]*"' contained
65 | syntax match num2 '"[0-9.]*"' contained
66 |
67 | " " matches names
68 | syntax match gene_name '"\<[0-9A-Za-z.-]*\>"' contained
69 | syntax match ont_name '"\<[0-9A-Za-z.-:]*\>"' contained
70 | syntax match havName '"\<[0-9A-Za-z.-]*\>"' contained
71 |
72 | "
73 | " " Highlighting / Theme Control
74 | " =========================================================
75 | highlight link Col1 chr
76 | highlight link Col2 keyword
77 | highlight link Col3 normal
78 | highlight link Col4 chrStart
79 | highlight link Col5 chrEnd
80 | highlight Col6 ctermfg=100
81 | highlight link Col7 strandNone
82 | highlight Col8 ctermfg=100
83 | highlight Col9 ctermfg=7
84 |
85 | highlight link strg quoteString
86 | highlight link ident keyword3
87 | highlight ens ctermfg=172
88 | highlight na ctermfg=59
89 | highlight link gene_type geneSymbol
90 | highlight link gene_id geneSymbol
91 | "highlight name ctermfg=118
92 | highlight link gene_name keyword
93 | highlight link havName keyword4
94 | highlight link ont_name keyword6
95 |
96 | highlight link num numeric
97 | highlight link num2 numeric2
98 |
99 | highlight link s exonLevel
100 | highlight link s2 transcriptLevel
101 | highlight link s3 geneLevel
102 | highlight link s4 start_codon
103 | highlight link s5 stop_codon
104 | highlight link s6 cds
105 | highlight link s7 utr
106 | highlight link s8 utr
107 | highlight link s9 utr
108 |
109 | highlight link plus strandPlus
110 | highlight link minus strandMinus
111 |
112 | highlight link zero keyword4
113 | highlight link one keyword5
114 | highlight link two keyword6
115 |
116 |
--------------------------------------------------------------------------------
/syntax/gedit/fasta.lang:
--------------------------------------------------------------------------------
1 |
2 |
16 |
17 |
18 | text/fasta
19 | *.fa,*.fasta,*.mfa,*.fas
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
56 |
57 |
58 |
59 | [Aa]++
60 |
61 |
62 | [Tt]++
63 |
64 |
65 | [Gg]++
66 |
67 |
68 | [Cc]++
69 |
70 |
71 | [Uu]++
72 |
73 |
74 | [XxNn]++
75 |
76 |
77 | [\-\.]++
78 |
79 |
80 |
81 |
82 | [Rr]++
83 |
84 |
85 | [Yy]++
86 |
87 |
88 | [Ss]++
89 |
90 |
91 | [Ww]++
92 |
93 |
94 | [Mm]++
95 |
96 |
97 | [Kk]++
98 |
99 |
100 | [Dd]++
101 |
102 |
103 | [Bb]++
104 |
105 |
106 | [Vv]++
107 |
108 |
109 | [Hh]++
110 |
111 |
112 |
113 |
114 |
115 |
116 |
--------------------------------------------------------------------------------
/syntax/gedit/fasta-hc.lang:
--------------------------------------------------------------------------------
1 |
2 |
16 |
17 |
18 | text/fastahc
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
56 |
57 |
58 |
59 | [Aa]++
60 |
61 |
62 | [Tt]++
63 |
64 |
65 | [Gg]++
66 |
67 |
68 | [Cc]++
69 |
70 |
71 | [Uu]++
72 |
73 |
74 | [XxNn]++
75 |
76 |
77 | [\-\.]++
78 |
79 |
80 |
81 |
82 | [Rr]++
83 |
84 |
85 | [Yy]++
86 |
87 |
88 | [Ss]++
89 |
90 |
91 | [Ww]++
92 |
93 |
94 | [Mm]++
95 |
96 |
97 | [Kk]++
98 |
99 |
100 | [Dd]++
101 |
102 |
103 | [Bb]++
104 |
105 |
106 | [Vv]++
107 |
108 |
109 | [Hh]++
110 |
111 |
112 |
113 |
114 |
115 |
116 |
--------------------------------------------------------------------------------
/examples/nt-seq/test_alignment1.mfa:
--------------------------------------------------------------------------------
1 | >Cryptosporidium_hominis/868-954
2 | AAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUCCGUAGUCUUAACCAUAAACUAUGC.CAACU
3 | .AGAGAUUGGAGGU.UGU.U....................
4 | >Yarrowia_lipolytica/859-941
5 | AAGAACGAAAGUUAGGGGAUCAAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCGUAAACUAUGC.CGACU
6 | .GAGAAUGGGUA.C.CG.......................
7 | >Thalassiosira_pseudonana/975-1060
8 | AAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUAC.CAUC.GUAGUCUUAACCAUAAACUAUGC.CGACU
9 | .CGGGAUUGGCGGU.UGU.U....................
10 | >Guillardia_theta/949-1034
11 | AAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAACUAUGC.CGACU
12 | .AGGGAUCAGUGGA.UGU.C....................
13 | >Aedes_albopictus/1036-1121
14 | AAGAACGAAAGUUAGAGGAUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUAACCGUAAACUAUGC.CAAUU
15 | .AGCAAUUGGGAGA.CGC.U....................
16 | >Cyanidioschyzon_merolae/969-1054
17 | AAGAACGAAAGUUAGGGGAUCGAAGACGAUUAGAUAC.CGUC.GUAGUCUUAACCAUAAACGAUGC.CGACU
18 | .CGGGAUCGGUGGAG.CA.C....................
19 | >Tetrahymena_thermophila/948-1030
20 | AAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACUAUAAACUAUAC.CGACU
21 | .CGGGAUCGGCUGG..A.......................
22 | >Dictyostelium_discoideum/969-1054
23 | AAGAACGAAAGUUUGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCCAAACUAUAAACUAUGU.CGACC
24 | .AGGGAUCGGUUAA.AAU.U....................
25 | >Plasmodium_falciparum/1039-1144
26 | AAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUAC.CGUC.GUAAUCUUAACCAUAAACUAUGC.CGACU
27 | .AGGUGUUGGAUGA.AAG.UGUUAAAAAUAAAAGUCAUCU
28 | >Schizosaccharomyces_pombe/985-1070
29 | AAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAACUAUGC.CGACU
30 | .AGGGAUCGGGCAA.UGU.U....................
31 | >Caenorhabditis_elegans/942-1025
32 | AAGAACGAAAGUCAGAGGUUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUGACCGUAAACGAUGC.CAUCU
33 | .CGCGAUUCGGAGG..G..U....................
34 | >Leishmania_major/1217-1306
35 | AAGAACCAAAGUGUGGAGAUCGAAGAUGAUUAGAGAC.CAUU.GUAGUCCACACUGCAAACGAUGA.CACCC
36 | .AUGAAUUGGGGAU.CUU.AUG......GG..........
37 | >Caenorhabditis_briggsae/935-1018
38 | AAGAACGAAAGUCAGAGGUUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUGACCGUAAACGAUGC.CAUCU
39 | .CGCGAUUCGGAGG..G..U....................
40 | >Saccharomyces_cerevisiae/970-1055
41 | AAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAACUAUGC.CGACU
42 | .AGGGAUCGGGUGG.UGU.U....................
43 | >Xenopus_laevis/989-1074
44 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAACGAUGC.CGACU
45 | .AGCGAUCCGGCGG.CGU.U....................
46 | >Eremothecium_gossypii/966-1051
47 | AAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAACUAUGC.CGACU
48 | .AGGGAUCGGGUGG.UGU.U....................
49 | >Trypanosoma_brucei/1219-1310
50 | AAGAACCAAAGUGUGGGGAUCAAAGAUGAUUAGAGAC.CAUU.GUAGUCCACACUGCAAACCAUGA.CACCC
51 | .AUGAAUUGGGGAACAUCAUUG......GG..........
52 | >Latimeria/979-1064 chalumnae
53 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAACGAUGC.CAACU
54 | .ACCGAUCCGGCGG.CGU.U....................
55 | >Adineta_vaga/970-1055
56 | AAGAACGAAAGUUUGAGGUUCGAAGACGAUUAGAUAC.CGUC.CUAGUUCAAACCAUAAACGUUGC.CAACU
57 | .GUCUUUUAGAUGC.GGU.U....................
58 | >Danio_rerio/1046-1131
59 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCGUAAACGAUGC.CGACC
60 | .CGCGAUCCGGCGG.CGU.U....................
61 | >Anolis_carolinses/980-1065
62 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAACGAUGC.CGACU
63 | .AGCGAUCCGGCGG.CGU.U....................
64 | >Gallus_gallus/985-1070
65 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAACGAUGC.CGACU
66 | .CGCGAUCCGGCGG.CGU.U....................
67 | >Oryza_sativa/975-1060
68 | AAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUAC.CGUC.CUAGUCUCAACCAUAAACGAUGC.CGACC
69 | .AGGGAUCGGCGGA.UGU.U....................
70 | >Arabidopsis_thaliana/974-1059
71 | AAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUAC.CGUC.CUAGUCUCAACCAUAAACGAUGC.CGACC
72 | .AGGGAUCAGCGGA.UGU.U....................
73 | >Homo_sapiens/1027-1112
74 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAACGAUGC.CGACC
75 | .GGCGAUGCGGCGG.CGU.U....................
76 | >Rattus_norvegicus/1031-1116
77 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAACGAUGC.CGACU
78 | .GGCGAUGCGGCGG.CGU.U....................
79 | >Monodelphis_domestica/1068-1155
80 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACUCGUC.GUAGUUCCGACCAUAAACGAUGCUCGACU
81 | .AGCGAUCCGGCGG.CGU.U....................
82 | >Mus_musculus/1029-1114
83 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAACGAUGC.CGACU
84 | .GGCGAUGCGGCGG.CGU.U....................
85 | >Drosophila_melanogaster/1057-1142
86 | AAGAACGAAAGUUAGAGGUUCGAAGGCGAUCAGAUAC.CGCC.CUAGUUCUAACCAUAAACGAUGC.CAGCU
87 | .AGCAAUUGGGUGU.AGC.U....................
88 | >Pan_troglodytes/1024-1109
89 | AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUG.GUAGUUCUGUCCAUAAACGAAGC.CGACU
90 | .GGCAACGUGGCGG.UGU.U....................
91 |
92 |
--------------------------------------------------------------------------------
/docs/install.md:
--------------------------------------------------------------------------------
1 | # Installing bioSyntax
2 |
3 | We're working on an installer to make this easier, but if you can't wait, here's how to get bioSyntax now.
4 |
5 | 1. [sublime](#sublime)
6 | 2. [gedit](#gedit)
7 | 3. [less](#less)
8 |
9 |
10 | ## sublime
11 | (Linux / Mac / Win)
12 |
13 | 0. Install [Sublime Text](http://www.sublimetext.com/)
14 | 1. Download the [bioMonokai Color Scheme](https://github.com/ababaian/bioSyntax/blob/master/dev/theme/sublime/Color%20Scheme%20-%20bioSyntax.sublime-package).
15 | 2. Copy it to your Sublime Text application packages folder:
16 | - **Linux**: `../sublime_text_3/Packages/`
17 | - **Windows**: `C:/Program Files/Sublime Text 3/Packages/`
18 | - **Mac**: `/Applications/Sublime Text.app/Contents/MacOS/Packages/`
19 | 3. Download the [bioSyntax sublime package](https://github.com/ababaian/bioSyntax/blob/master/syntax/bioSyntax_sublime_RELEASE.zip).
20 | 4. Unzip the `*.sublime-syntax` files into the Sublime Text Packages folder:
21 | - **Linux**: `~/.config/sublime-text-3/Packages/User/`
22 | - **Windows**: `%APPDATA%/Roaming/Sublime Text 3/Packages/`
23 | - **Mac**: `/Users/your_username/Library/Application Support/Sublime Text 3/Packages/`
24 | 5. Open Sublime Text and go select the bioSyntax (bioMonokai) theme
25 | `Preferences > Color Scheme > bioMonokai`
26 | 6. Formats should auto-detect; you can select a specific syntax at the drop-menu at the bottom-right corner of the window (e.g. Plain Text)
27 | 7. You now have pretty formats!
28 |
29 | ## gedit
30 | (Linux / Win)
31 | 1. Download the respective `*.lang` files you're interested in
32 | 2. Download the `bioKate.xml` style scheme
33 |
34 | 3. Change permissions to all readonly
35 | `chmod 0644 *.lang`
36 |
37 | 4. Copy the `bioKate.xml` style scheme to gtksoureview style folder
38 | `sudo cp bioKate.xml /usr/share/gtksourceview-3.0/styles/bioKate.xml`
39 |
40 | 5. Copy the `*.lang` file(s) to gtksourceview language spec folder
41 | `sudo cp fasta.lang /usr/share/gtksourceview-3.0/language-specs/fasta.lang`
42 |
43 | 6. Restart `gedit` and select the bioSyntax theme
44 | `Edit > Preferences > Font & Color > bioKate'`
45 | 7. You now have pretty formats!
46 |
47 | ## less
48 | (Linux)
49 |
50 | ### Install `source-highlight` (Ubuntu)
51 |
52 | 1) Install `source-highlight` to your system:
53 | ```
54 | sudo apt-get update
55 | sudo apt-get install source-highlight
56 | ```
57 | 2) Append these lines to your `~/.bashrc` and/or `~/.zshrc`
58 | ```
59 |
60 | ## Syntax highlighting in less
61 | ## For Ubuntu / Fedora
62 | export LESSOPEN="| /usr/share/source-highlight/src-hilite-lesspipe.sh %s"
63 | export LESS=" -R "
64 |
65 | alias less='less -NSi -# 10'
66 | alias more='less'
67 |
68 | # Explicit fasta / sam less call for piping
69 | # i.e: samtools view -h aligned_hits.bam | sam-less
70 | #
71 | alias fa-less='source-highlight -f esc --lang-def=fasta.lang --outlang-def=bioSyntax.outlang --style-file=fa.style | less'
72 | alias sam-less='source-highlight -f esc --lang-def=sam.lang --outlang-def=bioSyntax.outlang --style-file=sam.style | less'
73 | alias vcf-less='source-highlight -f esc --lang-def=vcf.lang --outlang-def=bioSyntax-vcf.outlang --style-file=vcf.style | less'
74 | ```
75 |
76 | **Note**: On different systems the `/usr/share/source-highlight/src-hilite-lesspipe.sh` may be installed to a different directory. (i.e CentOS: `export LESSOPEN="| /usr/bin/src-hilite-lesspipe.sh %s"`)
77 |
78 | ### Installing `bioSyntax` for less (Ubuntu)
79 |
80 | 1) Update the `src-hilite-lesspipe.sh` script in the source-highlight directory.
81 |
82 | ```
83 | # source-highlight directory on your system
84 | SRCDIR='/usr/share/source-highlight'
85 |
86 | cd $bioSyntax_PATH/syntax/less/
87 |
88 | sudo cp src-hilite-lesspipe_BIO.sh $SRCDIR/src-hilite-lesspipe.sh
89 | ```
90 |
91 | 2) Copy over the `*.lang`, `.outlang` and `.syntax` files to the source-highlight directory.
92 |
93 | ```
94 | #!/bin/bash
95 | # quickInstall.sh
96 | # Quick installer for less syntax
97 | # for testing purposes
98 |
99 | SRCDIR='/usr/share/source-highlight'
100 |
101 | # Copy over src-hilite script
102 | sudo cp src-hilite-lesspipe_BIO.sh $SRCDIR/src-hilite-lesspipe.sh
103 |
104 |
105 | # Copy over language files
106 | sudo cp fasta.lang $SRCDIR/
107 | sudo cp sam.lang $SRCDIR/
108 | sudo cp vcf.lang $SRCDIR/
109 |
110 | # Copy over syle files
111 | sudo cp fasta.style $SRCDIR/
112 | sudo cp sam.style $SRCDIR/
113 | sudo cp vcf.style $SRCDIR/
114 |
115 | # Copy over language files
116 | sudo cp bioSyntax.outlang $SRCDIR/
117 | sudo cp bioSyntax-vcf.outlang $SRCDIR/
118 | ```
119 |
120 | 3) Restart your computer for the `rc` file to update in your terminal.
--------------------------------------------------------------------------------
/examples/nt-seq/test_alignment1.clustal:
--------------------------------------------------------------------------------
1 | CLUSTAL
2 |
3 | Cryptosporidium_hominis/868-954 AAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUCCGUAGUCUUAACCAUAAA
4 | Yarrowia_lipolytica/859-941 AAGAACGAAAGUUAGGGGAUCAAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCGUAAA
5 | Thalassiosira_pseudonana/975-1060 AAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUAC.CAUC.GUAGUCUUAACCAUAAA
6 | Guillardia_theta/949-1034 AAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAA
7 | Aedes_albopictus/1036-1121 AAGAACGAAAGUUAGAGGAUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUAACCGUAAA
8 | Cyanidioschyzon_merolae/969-1054 AAGAACGAAAGUUAGGGGAUCGAAGACGAUUAGAUAC.CGUC.GUAGUCUUAACCAUAAA
9 | Tetrahymena_thermophila/948-1030 AAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACUAUAAA
10 | Dictyostelium_discoideum/969-1054 AAGAACGAAAGUUUGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCCAAACUAUAAA
11 | Plasmodium_falciparum/1039-1144 AAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUAC.CGUC.GUAAUCUUAACCAUAAA
12 | Schizosaccharomyces_pombe/985-1070 AAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAA
13 | Caenorhabditis_elegans/942-1025 AAGAACGAAAGUCAGAGGUUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUGACCGUAAA
14 | Leishmania_major/1217-1306 AAGAACCAAAGUGUGGAGAUCGAAGAUGAUUAGAGAC.CAUU.GUAGUCCACACUGCAAA
15 | Caenorhabditis_briggsae/935-1018 AAGAACGAAAGUCAGAGGUUCGAAGGCGAUUAGAUAC.CGCC.CUAGUUCUGACCGUAAA
16 | Saccharomyces_cerevisiae/970-1055 AAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAA
17 | Xenopus_laevis/989-1074 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
18 | Eremothecium_gossypii/966-1051 AAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUAC.CGUC.GUAGUCUUAACCAUAAA
19 | Trypanosoma_brucei/1219-1310 AAGAACCAAAGUGUGGGGAUCAAAGAUGAUUAGAGAC.CAUU.GUAGUCCACACUGCAAA
20 | Latimeria/979-1064 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
21 | Adineta_vaga/970-1055 AAGAACGAAAGUUUGAGGUUCGAAGACGAUUAGAUAC.CGUC.CUAGUUCAAACCAUAAA
22 | Danio_rerio/1046-1131 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCGUAAA
23 | Anolis_carolinses/980-1065 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
24 | Gallus_gallus/985-1070 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
25 | Oryza_sativa/975-1060 AAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUAC.CGUC.CUAGUCUCAACCAUAAA
26 | Arabidopsis_thaliana/974-1059 AAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUAC.CGUC.CUAGUCUCAACCAUAAA
27 | Homo_sapiens/1027-1112 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
28 | Rattus_norvegicus/1031-1116 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
29 | Monodelphis_domestica/1068-1155 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACUCGUC.GUAGUUCCGACCAUAAA
30 | Mus_musculus/1029-1114 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUC.GUAGUUCCGACCAUAAA
31 | Drosophila_melanogaster/1057-1142 AAGAACGAAAGUUAGAGGUUCGAAGGCGAUCAGAUAC.CGCC.CUAGUUCUAACCAUAAA
32 | Pan_troglodytes/1024-1109 AAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUAC.CGUG.GUAGUUCUGUCCAUAAA
33 |
34 | Cryptosporidium_hominis/868-954 CUAUGC.CAACU.AGAGAUUGGAGGU.UGU.U....................
35 | Yarrowia_lipolytica/859-941 CUAUGC.CGACU.GAGAAUGGGUA.C.CG.......................
36 | Thalassiosira_pseudonana/975-1060 CUAUGC.CGACU.CGGGAUUGGCGGU.UGU.U....................
37 | Guillardia_theta/949-1034 CUAUGC.CGACU.AGGGAUCAGUGGA.UGU.C....................
38 | Aedes_albopictus/1036-1121 CUAUGC.CAAUU.AGCAAUUGGGAGA.CGC.U....................
39 | Cyanidioschyzon_merolae/969-1054 CGAUGC.CGACU.CGGGAUCGGUGGAG.CA.C....................
40 | Tetrahymena_thermophila/948-1030 CUAUAC.CGACU.CGGGAUCGGCUGG..A.......................
41 | Dictyostelium_discoideum/969-1054 CUAUGU.CGACC.AGGGAUCGGUUAA.AAU.U....................
42 | Plasmodium_falciparum/1039-1144 CUAUGC.CGACU.AGGUGUUGGAUGA.AAG.UGUUAAAAAUAAAAGUCAUCU
43 | Schizosaccharomyces_pombe/985-1070 CUAUGC.CGACU.AGGGAUCGGGCAA.UGU.U....................
44 | Caenorhabditis_elegans/942-1025 CGAUGC.CAUCU.CGCGAUUCGGAGG..G..U....................
45 | Leishmania_major/1217-1306 CGAUGA.CACCC.AUGAAUUGGGGAU.CUU.AUG......GG..........
46 | Caenorhabditis_briggsae/935-1018 CGAUGC.CAUCU.CGCGAUUCGGAGG..G..U....................
47 | Saccharomyces_cerevisiae/970-1055 CUAUGC.CGACU.AGGGAUCGGGUGG.UGU.U....................
48 | Xenopus_laevis/989-1074 CGAUGC.CGACU.AGCGAUCCGGCGG.CGU.U....................
49 | Eremothecium_gossypii/966-1051 CUAUGC.CGACU.AGGGAUCGGGUGG.UGU.U....................
50 | Trypanosoma_brucei/1219-1310 CCAUGA.CACCC.AUGAAUUGGGGAACAUCAUUG......GG..........
51 | Latimeria/979-1064 CGAUGC.CAACU.ACCGAUCCGGCGG.CGU.U....................
52 | Adineta_vaga/970-1055 CGUUGC.CAACU.GUCUUUUAGAUGC.GGU.U....................
53 | Danio_rerio/1046-1131 CGAUGC.CGACC.CGCGAUCCGGCGG.CGU.U....................
54 | Anolis_carolinses/980-1065 CGAUGC.CGACU.AGCGAUCCGGCGG.CGU.U....................
55 | Gallus_gallus/985-1070 CGAUGC.CGACU.CGCGAUCCGGCGG.CGU.U....................
56 | Oryza_sativa/975-1060 CGAUGC.CGACC.AGGGAUCGGCGGA.UGU.U....................
57 | Arabidopsis_thaliana/974-1059 CGAUGC.CGACC.AGGGAUCAGCGGA.UGU.U....................
58 | Homo_sapiens/1027-1112 CGAUGC.CGACC.GGCGAUGCGGCGG.CGU.U....................
59 | Rattus_norvegicus/1031-1116 CGAUGC.CGACU.GGCGAUGCGGCGG.CGU.U....................
60 | Monodelphis_domestica/1068-1155 CGAUGCUCGACU.AGCGAUCCGGCGG.CGU.U....................
61 | Mus_musculus/1029-1114 CGAUGC.CGACU.GGCGAUGCGGCGG.CGU.U....................
62 | Drosophila_melanogaster/1057-1142 CGAUGC.CAGCU.AGCAAUUGGGUGU.AGC.U....................
63 | Pan_troglodytes/1024-1109 CGAAGC.CGACU.GGCAACGUGGCGG.UGU.U....................
64 |
--------------------------------------------------------------------------------
/syntax/gedit/fasta-clustal.lang:
--------------------------------------------------------------------------------
1 |
2 |
12 |
13 |
14 |
15 |
16 | text/fastza
17 | *.faa
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
57 |
58 |
59 | [Aa]++
60 |
61 |
62 |
63 | [Bb]++
64 |
65 |
66 |
67 | [Cc]++
68 |
69 |
70 |
71 | [Dd]++
72 |
73 |
74 |
75 | [Ee]++
76 |
77 |
78 |
79 | [Ff]++
80 |
81 |
82 |
83 | [Gg]++
84 |
85 |
86 |
87 | [Hh]++
88 |
89 |
90 |
91 | [Ii]++
92 |
93 |
94 |
95 | [Kk]++
96 |
97 |
98 |
99 | [Ll]++
100 |
101 |
102 |
103 | [Mm]++
104 |
105 |
106 |
107 | [Nn]++
108 |
109 |
110 |
111 | [Pp]++
112 |
113 |
114 |
115 | [Qq]++
116 |
117 |
118 |
119 | [Rr]++
120 |
121 |
122 |
123 | [Ss]++
124 |
125 |
126 |
127 | [Tt]++
128 |
129 |
130 |
131 | [Vv]++
132 |
133 |
134 |
135 | [Ww]++
136 |
137 |
138 |
139 | [Yy]++
140 |
141 |
142 |
143 | [Zz]++
144 |
145 |
146 |
147 | [Xx]++
148 |
149 |
150 |
151 | \*
152 |
153 |
154 |
155 | [\-\.]
156 |
157 |
158 |
159 |
160 |
161 |
162 |
--------------------------------------------------------------------------------
/syntax/vim/vcf.vim:
--------------------------------------------------------------------------------
1 | " Vim syntax file
2 | " Language: VCF v4.3
3 | " Filetypes: .vcf
4 | " Maintainer: bioSyntax
5 | " Version: v0
6 |
7 | "TODO
8 | " Set vim sync mode so it can deal with long lines
9 |
10 | if exists("syntax_on")
11 | syntax reset
12 | " VCF syntax is per-line so restrict context to one line
13 | syntax sync minlines=1
14 | colorscheme bioSyntax
15 | " VCF are wide files; remove word-wrapping
16 | set nowrap
17 | endif
18 |
19 |
20 | " Syntax Organization
21 | " Use 'containedin=' when a syntax defintion must only be matched within only one region
22 | " Use 'contained' when a syntax definition may be matched from two or more regions
23 | " All region definitions are limited to 'oneline' in VCF
24 |
25 | " VCF DATA Selection
26 | " =========================================================
27 | "
28 |
29 | " Column 1: LONG LINE FAILSAFE (no highlight)
30 | syntax region FAILSAFE start='^' end='$' contains=COL2
31 |
32 | " Column 1: CHROM
33 | syntax region chr start='^[^#]' end='$' oneline contains=COL2
34 |
35 | " Column 2: POS
36 | syntax region COL2 matchgroup=COL2 start='\t' end='\n\@=' oneline contained contains=COL3
37 | syntax region chrStart start='\t\@<=[0-9]' end='[\n\t]\@=' contained containedin=COL2
38 |
39 | " Column 3: ID
40 | syntax region COL3 matchgroup=COL3 start='\t' end='\n\@=' oneline contained contains=COL4,nt_
41 | syntax region ID start='\t\@<=\S' end='[\n\t]\@=' containedin=COL3
42 |
43 |
44 | " Column 4: REF
45 | syntax region COL4 matchgroup=COL4 start='\t' end='\n\@=' oneline contained contains=COL5,ntA,ntT,ntG,ntC,ntN,nt_
46 | syntax match ntA '[Aa]' contained
47 | syntax match ntT '[Tt]' contained
48 | syntax match ntG '[Gg]' contained
49 | syntax match ntC '[Cc]' contained
50 | syntax match ntN '[Nn]' contained
51 | syntax match nt_ '\.' contained
52 |
53 | " Column 5: ALT
54 | syntax region COL5 matchgroup=COL5 start='\t' end='\n\@=' oneline contained contains=COL6,ntA,ntT,ntG,ntC,ntN,nt_
55 |
56 | " Column 6: QUAL
57 | syntax region COL6 matchgroup=COL6 start='\t' end='\n\@=' oneline contained contains=COL7
58 | syntax region QUAL start='\t\@<=[0-9]' end='[\n\t]\@=' oneline containedin=COL6
59 |
60 | " Column 7: FILTER
61 | syntax region COL7 matchgroup=COL7 start='\t' end='\n\@=' oneline contained contains=COL8,bon,mal,nt_
62 |
63 | " Column 8: INFO
64 | syntax region COL8 matchgroup=COL8 start='\t' end='\n\@=' oneline contained contains=COL9
65 | syntax region INFOtag start='\t\@<=[A-Za-z]' end='[\n\t]\@=' oneline containedin=COL8 contains=numeric,string
66 |
67 | " Column 9: FORMAT
68 | syntax region COL9 matchgroup=COL9 start='\t' end='\n\@=' oneline contained contains=COL10
69 | syntax region FORMATtag start='\t\@<=[A-Za-z]' end='[\n\t]\@=' oneline containedin=COL9
70 |
71 | " Column 10+: DATA
72 | syntax region COL10 matchgroup=COL10 start='\t' end='\n\@=' oneline contained
73 |
74 | " Data Start Header Lines
75 | syntax match header '^#CHROM.\+'
76 |
77 |
78 |
79 | " VCF Header Selection
80 | " =========================================================
81 | "
82 | syntax region comment start='^##' end='\n' oneline contains=header,FILTER,FORMAT,INFO,reference
83 |
84 | " First Line Header
85 | syntax region header start='fileformat' end='\n' oneline contained
86 |
87 | " FILTER Lines
88 | syntax region FILTER start='FILTER' end='\n' oneline contained contains=string,stringQuote,numeric
89 |
90 | " FORMAT Lines
91 | syntax region FORMAT start='FORMAT' end='\n' oneline contained contains=string,stringQuote,numeric
92 |
93 | " INFO Lines
94 | syntax region INFO start='INFO' end='\n' oneline contained contains=string,stringQuote,numeric
95 |
96 | " Non-specification Lines
97 | syntax region reference start='\(contig=\|reference=\)' end='\n' oneline contained
98 |
99 | " Header Submatches (ID, Other Tags, Quote Strings)
100 | syntax region numeric start='=\@<=[^<\"]\@=' end='[,;\t]\@=' oneline contained
101 | syntax region string start='\(ID=\)\@<=' end='[,;\t]\@=' oneline contained
102 | syntax region stringQuote start='\"' end='\"' oneline contained
103 |
104 |
105 | " Highlighting / Local Link Controls
106 | " =========================================================
107 | highlight link FILTERtag FILTER
108 | highlight link FORMATtag FORMAT
109 | highlight link INFOtag INFO
110 |
111 |
112 | highlight link QUAL numeric
113 | highlight link ID string
114 |
115 | highlight link FILTER keyword1
116 | highlight link FORMAT keyword2
117 | highlight link INFO keyword3
118 | highlight link reference chrStart
119 |
120 | highlight link nt_ ntX
121 | highlight link stringQuote quoteString
122 |
123 | " Highlighting / Global Theme Control
124 | " =========================================================
125 | " (TO CHANGE THEME COLORS, MODIFY VALUES BELOW ONLY)
126 | "
127 | "highlight numeric ctermfg=31
128 | "highlight string ctermfg=160
129 | "highlight stringQuote ctermfg=160 cterm=italic
130 | "highlight comment ctermfg=08
131 |
132 | "highlight header ctermfg=08 ctermbg=250 cterm=bold
133 |
134 | "highlight keyword1 ctermfg=130 " Orange
135 | "highlight keyword2 ctermfg=89 " Purple Dark
136 | "highlight keyword3 ctermfg=172 " Yellow
137 |
138 | "highlight chr ctermfg=28 cterm=bold
139 | "highlight chrStart ctermfg=28
140 |
141 | "highlight ntA ctermfg=Black ctermbg=10 guibg=#272822
142 | "highlight ntG ctermfg=Black ctermbg=214 guibg=#FF8C00
143 | "highlight ntC ctermfg=Black ctermbg=9 guibg=#2A0AFD
144 | "highlight ntT ctermfg=Black ctermbg=33 guibg=#FD0A0A
145 | "highlight ntN ctermfg=Black ctermbg=255 guibg=#FD0A0A
146 | "highlight nt_ ctermfg=Black ctermbg=255 guibg=#000000
147 |
--------------------------------------------------------------------------------
/syntax/gedit/fasta-zappo.lang:
--------------------------------------------------------------------------------
1 |
2 |
12 |
13 |
14 |
15 |
16 | text/fastza
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
57 |
58 |
59 | [Aa]++
60 |
61 |
62 |
63 | [Bb]++
64 |
65 |
66 |
67 | [Cc]++
68 |
69 |
70 |
71 | [Dd]++
72 |
73 |
74 |
75 | [Ee]++
76 |
77 |
78 |
79 | [Ff]++
80 |
81 |
82 |
83 | [Gg]++
84 |
85 |
86 |
87 | [Hh]++
88 |
89 |
90 |
91 | [Ii]++
92 |
93 |
94 |
95 | [Kk]++
96 |
97 |
98 |
99 | [Ll]++
100 |
101 |
102 |
103 | [Mm]++
104 |
105 |
106 |
107 | [Nn]++
108 |
109 |
110 |
111 | [Pp]++
112 |
113 |
114 |
115 | [Qq]++
116 |
117 |
118 |
119 | [Rr]++
120 |
121 |
122 |
123 | [Ss]++
124 |
125 |
126 |
127 | [Tt]++
128 |
129 |
130 |
131 | [Vv]++
132 |
133 |
134 |
135 | [Ww]++
136 |
137 |
138 |
139 | [Yy]++
140 |
141 |
142 |
143 | [Zz]++
144 |
145 |
146 |
147 | [Xx]++
148 |
149 |
150 |
151 | \*
152 |
153 |
154 |
155 | [\-\.]
156 |
157 |
158 |
159 |
160 |
161 |
162 |
--------------------------------------------------------------------------------
/syntax/gedit/fasta-taylor.lang:
--------------------------------------------------------------------------------
1 |
2 |
12 |
13 |
14 |
15 |
16 | text/fastay
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
57 |
58 |
59 | [Aa]++
60 |
61 |
62 |
63 | [Bb]++
64 |
65 |
66 |
67 | [Cc]++
68 |
69 |
70 |
71 | [Dd]++
72 |
73 |
74 |
75 | [Ee]++
76 |
77 |
78 |
79 | [Ff]++
80 |
81 |
82 |
83 | [Gg]++
84 |
85 |
86 |
87 | [Hh]++
88 |
89 |
90 |
91 | [Ii]++
92 |
93 |
94 |
95 | [Kk]++
96 |
97 |
98 |
99 | [Ll]++
100 |
101 |
102 |
103 | [Mm]++
104 |
105 |
106 |
107 | [Nn]++
108 |
109 |
110 |
111 | [Pp]++
112 |
113 |
114 |
115 | [Qq]++
116 |
117 |
118 |
119 | [Rr]++
120 |
121 |
122 |
123 | [Ss]++
124 |
125 |
126 |
127 | [Tt]++
128 |
129 |
130 |
131 | [Vv]++
132 |
133 |
134 |
135 | [Ww]++
136 |
137 |
138 |
139 | [Yy]++
140 |
141 |
142 |
143 | [Zz]++
144 |
145 |
146 |
147 | [Xx]++
148 |
149 |
150 |
151 | \*
152 |
153 |
154 |
155 | [\-\.]
156 |
157 |
158 |
159 |
160 |
161 |
162 |
--------------------------------------------------------------------------------
/syntax/gedit/fasta-hydrophobicity.lang:
--------------------------------------------------------------------------------
1 |
2 |
12 |
13 |
14 |
15 |
16 | text/fasthy
17 |
18 |
19 |
20 |
21 |
22 |
23 |
24 |
25 |
26 |
27 |
28 |
29 |
30 |
31 |
32 |
33 |
34 |
35 |
36 |
37 |
38 |
39 |
40 |
41 |
42 |
43 |
44 |
45 |
46 |
47 |
48 |
49 |
50 |
51 |
52 |
53 |
57 |
58 |
59 | [Aa]++
60 |
61 |
62 |
63 | [Bb]++
64 |
65 |
66 |
67 | [Cc]++
68 |
69 |
70 |
71 | [Dd]++
72 |
73 |
74 |
75 | [Ee]++
76 |
77 |
78 |
79 | [Ff]++
80 |
81 |
82 |
83 | [Gg]++
84 |
85 |
86 |
87 | [Hh]++
88 |
89 |
90 |
91 | [Ii]++
92 |
93 |
94 |
95 | [Kk]++
96 |
97 |
98 |
99 | [Ll]++
100 |
101 |
102 |
103 | [Mm]++
104 |
105 |
106 |
107 | [Nn]++
108 |
109 |
110 |
111 | [Pp]++
112 |
113 |
114 |
115 | [Qq]++
116 |
117 |
118 |
119 | [Rr]++
120 |
121 |
122 |
123 | [Ss]++
124 |
125 |
126 |
127 | [Tt]++
128 |
129 |
130 |
131 | [Vv]++
132 |
133 |
134 |
135 | [Ww]++
136 |
137 |
138 |
139 | [Yy]++
140 |
141 |
142 |
143 | [Zz]++
144 |
145 |
146 |
147 | [Xx]++
148 |
149 |
150 |
151 | \*
152 |
153 |
154 |
155 | [\-\.]
156 |
157 |
158 |
159 |
160 |
161 |
162 |
--------------------------------------------------------------------------------
/examples/annot/test1.bed:
--------------------------------------------------------------------------------
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10 | chr5 149439015 149439073 L2c 232 +
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14 | chr5 149441749 149441810 (TCCA)n 294 +
15 | chr5 149441824 149442183 L1MB2 1886 -
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44 | chr5 149453224 149453342 MIR3 249 +
45 | chr5 149453382 149453405 (CA)n 186 +
46 | chr5 149453473 149453867 MLT1K 867 +
47 | chr5 149453868 149454036 AluSc8 1338 -
48 | chr5 149454288 149454770 L2c 269 +
49 | chr5 149454755 149454940 L2a 318 +
50 | chr5 149454925 149455333 L2a 971 +
51 | chr5 149455639 149455726 L2c 204 +
52 | chr5 149455884 149455960 (TCTA)n 595 +
53 | chr5 149455962 149456091 MIR 405 -
54 | chr5 149456200 149456504 L2c 393 +
55 | chr5 149457035 149457224 MIRb 589 +
56 | chr5 149457477 149457561 MIRb 186 +
57 | chr5 149458003 149458616 L2a 546 +
58 | chr5 149458655 149458757 MIR3 257 -
59 | chr5 149459163 149459321 L2a 292 +
60 | chr5 149460023 149460252 MIRb 442 +
61 | chr5 149461149 149461290 MIR 450 +
62 | chr5 149462194 149462373 MIRb 526 +
63 | chr5 149462912 149462964 (CA)n 468 +
64 | chr5 149463207 149463617 MER4C 2567 +
65 | chr5 149463618 149463906 AluSx1 1976 +
66 | chr5 149463906 149464035 (GGAA)n 867 +
67 | chr5 149464035 149464314 AluSg4 2142 -
68 | chr5 149464329 149464352 AT_rich 23 +
69 | chr5 149464458 149464553 L1ME2 344 +
70 | chr5 149464559 149464856 AluSx 2265 +
71 | chr5 149465439 149465602 MER5A1 710 +
72 | chr5 149465634 149465787 MIR3 312 -
73 | chr5 149466442 149466535 MER21B 465 +
74 | chr5 149466540 149466642 FRAM 621 -
75 | chr5 149466642 149466844 MER21B 605 +
76 | chr5 149466885 149467106 MIR 711 -
77 | chr5 149467191 149467284 HAL1 299 -
78 | chr5 149467284 149467598 AluJb 2063 -
79 | chr5 149467672 149467729 (TG)n 206 +
80 | chr5 149467779 149468084 L1MB5 7061 +
81 | chr5 149468084 149468396 AluSz 2414 -
82 | chr5 149468396 149468584 L1MB5 7061 +
83 | chr5 149468584 149468604 (CAAAA)n 180 +
84 | chr5 149468604 149469848 L1MB5 7061 +
85 | chr5 149469868 149470132 L1ME1 851 -
86 | chr5 149470268 149470541 L1PA17 1074 +
87 | chr5 149470546 149471340 L1MB5 3725 +
88 | chr5 149471332 149471600 L1ME1 481 +
89 | chr5 149471603 149471816 MER58A 1132 -
90 | chr5 149471921 149472015 MER44A 1334 -
91 | chr5 149472015 149472372 THE1B 2454 -
92 | chr5 149472372 149472576 MER44A 1334 -
93 | chr5 149472636 149472940 AluSx1 2263 -
94 | chr5 149472940 149473188 L1ME1 509 +
95 | chr5 149473188 149473344 L1MA6 1058 +
96 | chr5 149473344 149473642 AluSq2 2309 +
97 | chr5 149473642 149473674 L1MA6 1058 +
98 | chr5 149473674 149473842 L1ME1 729 +
99 | chr5 149474694 149475670 L1ME1 5852 +
100 | chr5 149475670 149475980 AluSq2 2308 +
101 | chr5 149475980 149476543 L1ME1 5852 +
102 | chr5 149476543 149476834 AluJr4 1547 +
103 | chr5 149476834 149477968 L1ME1 5852 +
104 | chr5 149477968 149478067 HY3 747 +
105 | chr5 149478067 149478453 L1ME1 5852 +
106 | chr5 149478453 149478770 AluSq2 2246 -
107 | chr5 149478770 149479455 L1ME1 2747 +
108 | chr5 149479465 149479621 L1ME3B 605 +
109 | chr5 149479630 149479752 FLAM_A 760 +
110 | chr5 149479853 149480065 AluY 1770 -
111 | chr5 149480134 149480482 L1ME3B 1097 +
112 | chr5 149480486 149480548 L1M5 228 -
113 | chr5 149480555 149481018 MLT1H 924 +
114 | chr5 149481444 149482022 L1ME4a 1241 -
115 | chr5 149482043 149482341 AluSx1 2252 -
116 | chr5 149482355 149482537 L1MC 324 -
117 | chr5 149482541 149482739 MIRc 460 -
118 | chr5 149482850 149483053 L3 271 -
119 | chr5 149483150 149483407 L2c 284 -
120 | chr5 149483493 149483639 MER5A 287 +
121 | chr5 149484092 149484265 MIRb 735 -
122 | chr5 149484319 149484353 (TGAA)n 205 +
123 | chr5 149484432 149484629 AluSx 2051 -
124 | chr5 149484629 149484926 AluSc8 2333 +
125 | chr5 149484926 149484948 (TA)n 198 +
126 | chr5 149484948 149485078 AluSx 2051 -
127 | chr5 149485080 149485383 AluJr 1749 -
128 | chr5 149485391 149485636 MIR 921 -
129 | chr5 149486497 149486647 L2b 184 +
130 | chr5 149486715 149486879 L2a 213 -
131 | chr5 149486884 149486975 MER94 306 -
132 | chr5 149486981 149487211 MIR 707 -
133 | chr5 149487247 149487367 MIRb 291 +
134 | chr5 149487414 149487727 L2b 391 -
135 | chr5 149487935 149488132 L2b 297 -
136 | chr5 149488786 149488877 MIRb 295 +
137 | chr5 149489005 149489225 MER113 485 +
138 | chr5 149489296 149489465 L1ME4a 392 +
139 | chr5 149489465 149490000 LTR10A 2737 +
140 | chr5 149490026 149490246 L1ME4a 326 +
141 | chr5 149491142 149491221 MIR3 195 +
142 | chr5 149491221 149491318 MIRb 374 +
143 | chr5 149491358 149491433 LTR24B 448 +
144 | chr5 149491544 149491794 LTR24B 458 +
145 | chr5 149491835 149491961 MIR 410 +
146 | chr5 149491994 149492121 MIR3 242 -
147 | chr5 149492804 149492899 C-rich 213 +
148 | chr5 149492837 149492894 CT-rich 286 +
149 |
--------------------------------------------------------------------------------
/docs/Gemfile.lock:
--------------------------------------------------------------------------------
1 | GEM
2 | remote: https://rubygems.org/
3 | specs:
4 | activesupport (4.2.8)
5 | i18n (~> 0.7)
6 | minitest (~> 5.1)
7 | thread_safe (~> 0.3, >= 0.3.4)
8 | tzinfo (~> 1.1)
9 | addressable (2.5.1)
10 | public_suffix (~> 2.0, >= 2.0.2)
11 | coffee-script (2.4.1)
12 | coffee-script-source
13 | execjs
14 | coffee-script-source (1.12.2)
15 | colorator (1.1.0)
16 | ethon (0.10.1)
17 | ffi (>= 1.3.0)
18 | execjs (2.7.0)
19 | faraday (0.12.1)
20 | multipart-post (>= 1.2, < 3)
21 | ffi (1.9.18)
22 | forwardable-extended (2.6.0)
23 | gemoji (3.0.0)
24 | github-pages (138)
25 | activesupport (= 4.2.8)
26 | github-pages-health-check (= 1.3.3)
27 | jekyll (= 3.4.3)
28 | jekyll-avatar (= 0.4.2)
29 | jekyll-coffeescript (= 1.0.1)
30 | jekyll-default-layout (= 0.1.4)
31 | jekyll-feed (= 0.9.2)
32 | jekyll-gist (= 1.4.0)
33 | jekyll-github-metadata (= 2.3.1)
34 | jekyll-mentions (= 1.2.0)
35 | jekyll-optional-front-matter (= 0.1.2)
36 | jekyll-paginate (= 1.1.0)
37 | jekyll-readme-index (= 0.1.0)
38 | jekyll-redirect-from (= 0.12.1)
39 | jekyll-relative-links (= 0.4.0)
40 | jekyll-sass-converter (= 1.5.0)
41 | jekyll-seo-tag (= 2.2.3)
42 | jekyll-sitemap (= 1.0.0)
43 | jekyll-swiss (= 0.4.0)
44 | jekyll-theme-architect (= 0.0.4)
45 | jekyll-theme-cayman (= 0.0.4)
46 | jekyll-theme-dinky (= 0.0.4)
47 | jekyll-theme-hacker (= 0.0.4)
48 | jekyll-theme-leap-day (= 0.0.4)
49 | jekyll-theme-merlot (= 0.0.4)
50 | jekyll-theme-midnight (= 0.0.4)
51 | jekyll-theme-minimal (= 0.0.4)
52 | jekyll-theme-modernist (= 0.0.4)
53 | jekyll-theme-primer (= 0.1.8)
54 | jekyll-theme-slate (= 0.0.4)
55 | jekyll-theme-tactile (= 0.0.4)
56 | jekyll-theme-time-machine (= 0.0.4)
57 | jekyll-titles-from-headings (= 0.1.5)
58 | jemoji (= 0.8.0)
59 | kramdown (= 1.13.2)
60 | liquid (= 3.0.6)
61 | listen (= 3.0.6)
62 | mercenary (~> 0.3)
63 | minima (= 2.1.1)
64 | rouge (= 1.11.1)
65 | terminal-table (~> 1.4)
66 | github-pages-health-check (1.3.3)
67 | addressable (~> 2.3)
68 | net-dns (~> 0.8)
69 | octokit (~> 4.0)
70 | public_suffix (~> 2.0)
71 | typhoeus (~> 0.7)
72 | html-pipeline (2.5.0)
73 | activesupport (>= 2)
74 | nokogiri (>= 1.4)
75 | i18n (0.8.1)
76 | jekyll (3.4.3)
77 | addressable (~> 2.4)
78 | colorator (~> 1.0)
79 | jekyll-sass-converter (~> 1.0)
80 | jekyll-watch (~> 1.1)
81 | kramdown (~> 1.3)
82 | liquid (~> 3.0)
83 | mercenary (~> 0.3.3)
84 | pathutil (~> 0.9)
85 | rouge (~> 1.7)
86 | safe_yaml (~> 1.0)
87 | jekyll-avatar (0.4.2)
88 | jekyll (~> 3.0)
89 | jekyll-coffeescript (1.0.1)
90 | coffee-script (~> 2.2)
91 | jekyll-default-layout (0.1.4)
92 | jekyll (~> 3.0)
93 | jekyll-feed (0.9.2)
94 | jekyll (~> 3.3)
95 | jekyll-gist (1.4.0)
96 | octokit (~> 4.2)
97 | jekyll-github-metadata (2.3.1)
98 | jekyll (~> 3.1)
99 | octokit (~> 4.0, != 4.4.0)
100 | jekyll-mentions (1.2.0)
101 | activesupport (~> 4.0)
102 | html-pipeline (~> 2.3)
103 | jekyll (~> 3.0)
104 | jekyll-optional-front-matter (0.1.2)
105 | jekyll (~> 3.0)
106 | jekyll-paginate (1.1.0)
107 | jekyll-readme-index (0.1.0)
108 | jekyll (~> 3.0)
109 | jekyll-redirect-from (0.12.1)
110 | jekyll (~> 3.3)
111 | jekyll-relative-links (0.4.0)
112 | jekyll (~> 3.3)
113 | jekyll-sass-converter (1.5.0)
114 | sass (~> 3.4)
115 | jekyll-seo-tag (2.2.3)
116 | jekyll (~> 3.3)
117 | jekyll-sitemap (1.0.0)
118 | jekyll (~> 3.3)
119 | jekyll-swiss (0.4.0)
120 | jekyll-theme-architect (0.0.4)
121 | jekyll (~> 3.3)
122 | jekyll-theme-cayman (0.0.4)
123 | jekyll (~> 3.3)
124 | jekyll-theme-dinky (0.0.4)
125 | jekyll (~> 3.3)
126 | jekyll-theme-hacker (0.0.4)
127 | jekyll (~> 3.3)
128 | jekyll-theme-leap-day (0.0.4)
129 | jekyll (~> 3.3)
130 | jekyll-theme-merlot (0.0.4)
131 | jekyll (~> 3.3)
132 | jekyll-theme-midnight (0.0.4)
133 | jekyll (~> 3.3)
134 | jekyll-theme-minimal (0.0.4)
135 | jekyll (~> 3.3)
136 | jekyll-theme-modernist (0.0.4)
137 | jekyll (~> 3.3)
138 | jekyll-theme-primer (0.1.8)
139 | jekyll (~> 3.3)
140 | jekyll-theme-slate (0.0.4)
141 | jekyll (~> 3.3)
142 | jekyll-theme-tactile (0.0.4)
143 | jekyll (~> 3.3)
144 | jekyll-theme-time-machine (0.0.4)
145 | jekyll (~> 3.3)
146 | jekyll-titles-from-headings (0.1.5)
147 | jekyll (~> 3.3)
148 | jekyll-watch (1.5.0)
149 | listen (~> 3.0, < 3.1)
150 | jemoji (0.8.0)
151 | activesupport (~> 4.0)
152 | gemoji (~> 3.0)
153 | html-pipeline (~> 2.2)
154 | jekyll (>= 3.0)
155 | kramdown (1.13.2)
156 | liquid (3.0.6)
157 | listen (3.0.6)
158 | rb-fsevent (>= 0.9.3)
159 | rb-inotify (>= 0.9.7)
160 | mercenary (0.3.6)
161 | mini_portile2 (2.1.0)
162 | minima (2.1.1)
163 | jekyll (~> 3.3)
164 | minitest (5.10.2)
165 | multipart-post (2.0.0)
166 | net-dns (0.8.0)
167 | nokogiri (1.7.2)
168 | mini_portile2 (~> 2.1.0)
169 | octokit (4.7.0)
170 | sawyer (~> 0.8.0, >= 0.5.3)
171 | pathutil (0.14.0)
172 | forwardable-extended (~> 2.6)
173 | public_suffix (2.0.5)
174 | rb-fsevent (0.9.8)
175 | rb-inotify (0.9.8)
176 | ffi (>= 0.5.0)
177 | rouge (1.11.1)
178 | safe_yaml (1.0.4)
179 | sass (3.4.23)
180 | sawyer (0.8.1)
181 | addressable (>= 2.3.5, < 2.6)
182 | faraday (~> 0.8, < 1.0)
183 | terminal-table (1.8.0)
184 | unicode-display_width (~> 1.1, >= 1.1.1)
185 | thread_safe (0.3.6)
186 | typhoeus (0.8.0)
187 | ethon (>= 0.8.0)
188 | tzinfo (1.2.3)
189 | thread_safe (~> 0.1)
190 | unicode-display_width (1.2.1)
191 |
192 | PLATFORMS
193 | ruby
194 |
195 | DEPENDENCIES
196 | github-pages
197 | jekyll-redirect-from
198 |
199 | BUNDLED WITH
200 | 1.14.6
201 |
--------------------------------------------------------------------------------
/docs/_site/Gemfile.lock:
--------------------------------------------------------------------------------
1 | GEM
2 | remote: https://rubygems.org/
3 | specs:
4 | activesupport (4.2.8)
5 | i18n (~> 0.7)
6 | minitest (~> 5.1)
7 | thread_safe (~> 0.3, >= 0.3.4)
8 | tzinfo (~> 1.1)
9 | addressable (2.5.1)
10 | public_suffix (~> 2.0, >= 2.0.2)
11 | coffee-script (2.4.1)
12 | coffee-script-source
13 | execjs
14 | coffee-script-source (1.12.2)
15 | colorator (1.1.0)
16 | ethon (0.10.1)
17 | ffi (>= 1.3.0)
18 | execjs (2.7.0)
19 | faraday (0.12.1)
20 | multipart-post (>= 1.2, < 3)
21 | ffi (1.9.18)
22 | forwardable-extended (2.6.0)
23 | gemoji (3.0.0)
24 | github-pages (138)
25 | activesupport (= 4.2.8)
26 | github-pages-health-check (= 1.3.3)
27 | jekyll (= 3.4.3)
28 | jekyll-avatar (= 0.4.2)
29 | jekyll-coffeescript (= 1.0.1)
30 | jekyll-default-layout (= 0.1.4)
31 | jekyll-feed (= 0.9.2)
32 | jekyll-gist (= 1.4.0)
33 | jekyll-github-metadata (= 2.3.1)
34 | jekyll-mentions (= 1.2.0)
35 | jekyll-optional-front-matter (= 0.1.2)
36 | jekyll-paginate (= 1.1.0)
37 | jekyll-readme-index (= 0.1.0)
38 | jekyll-redirect-from (= 0.12.1)
39 | jekyll-relative-links (= 0.4.0)
40 | jekyll-sass-converter (= 1.5.0)
41 | jekyll-seo-tag (= 2.2.3)
42 | jekyll-sitemap (= 1.0.0)
43 | jekyll-swiss (= 0.4.0)
44 | jekyll-theme-architect (= 0.0.4)
45 | jekyll-theme-cayman (= 0.0.4)
46 | jekyll-theme-dinky (= 0.0.4)
47 | jekyll-theme-hacker (= 0.0.4)
48 | jekyll-theme-leap-day (= 0.0.4)
49 | jekyll-theme-merlot (= 0.0.4)
50 | jekyll-theme-midnight (= 0.0.4)
51 | jekyll-theme-minimal (= 0.0.4)
52 | jekyll-theme-modernist (= 0.0.4)
53 | jekyll-theme-primer (= 0.1.8)
54 | jekyll-theme-slate (= 0.0.4)
55 | jekyll-theme-tactile (= 0.0.4)
56 | jekyll-theme-time-machine (= 0.0.4)
57 | jekyll-titles-from-headings (= 0.1.5)
58 | jemoji (= 0.8.0)
59 | kramdown (= 1.13.2)
60 | liquid (= 3.0.6)
61 | listen (= 3.0.6)
62 | mercenary (~> 0.3)
63 | minima (= 2.1.1)
64 | rouge (= 1.11.1)
65 | terminal-table (~> 1.4)
66 | github-pages-health-check (1.3.3)
67 | addressable (~> 2.3)
68 | net-dns (~> 0.8)
69 | octokit (~> 4.0)
70 | public_suffix (~> 2.0)
71 | typhoeus (~> 0.7)
72 | html-pipeline (2.5.0)
73 | activesupport (>= 2)
74 | nokogiri (>= 1.4)
75 | i18n (0.8.1)
76 | jekyll (3.4.3)
77 | addressable (~> 2.4)
78 | colorator (~> 1.0)
79 | jekyll-sass-converter (~> 1.0)
80 | jekyll-watch (~> 1.1)
81 | kramdown (~> 1.3)
82 | liquid (~> 3.0)
83 | mercenary (~> 0.3.3)
84 | pathutil (~> 0.9)
85 | rouge (~> 1.7)
86 | safe_yaml (~> 1.0)
87 | jekyll-avatar (0.4.2)
88 | jekyll (~> 3.0)
89 | jekyll-coffeescript (1.0.1)
90 | coffee-script (~> 2.2)
91 | jekyll-default-layout (0.1.4)
92 | jekyll (~> 3.0)
93 | jekyll-feed (0.9.2)
94 | jekyll (~> 3.3)
95 | jekyll-gist (1.4.0)
96 | octokit (~> 4.2)
97 | jekyll-github-metadata (2.3.1)
98 | jekyll (~> 3.1)
99 | octokit (~> 4.0, != 4.4.0)
100 | jekyll-mentions (1.2.0)
101 | activesupport (~> 4.0)
102 | html-pipeline (~> 2.3)
103 | jekyll (~> 3.0)
104 | jekyll-optional-front-matter (0.1.2)
105 | jekyll (~> 3.0)
106 | jekyll-paginate (1.1.0)
107 | jekyll-readme-index (0.1.0)
108 | jekyll (~> 3.0)
109 | jekyll-redirect-from (0.12.1)
110 | jekyll (~> 3.3)
111 | jekyll-relative-links (0.4.0)
112 | jekyll (~> 3.3)
113 | jekyll-sass-converter (1.5.0)
114 | sass (~> 3.4)
115 | jekyll-seo-tag (2.2.3)
116 | jekyll (~> 3.3)
117 | jekyll-sitemap (1.0.0)
118 | jekyll (~> 3.3)
119 | jekyll-swiss (0.4.0)
120 | jekyll-theme-architect (0.0.4)
121 | jekyll (~> 3.3)
122 | jekyll-theme-cayman (0.0.4)
123 | jekyll (~> 3.3)
124 | jekyll-theme-dinky (0.0.4)
125 | jekyll (~> 3.3)
126 | jekyll-theme-hacker (0.0.4)
127 | jekyll (~> 3.3)
128 | jekyll-theme-leap-day (0.0.4)
129 | jekyll (~> 3.3)
130 | jekyll-theme-merlot (0.0.4)
131 | jekyll (~> 3.3)
132 | jekyll-theme-midnight (0.0.4)
133 | jekyll (~> 3.3)
134 | jekyll-theme-minimal (0.0.4)
135 | jekyll (~> 3.3)
136 | jekyll-theme-modernist (0.0.4)
137 | jekyll (~> 3.3)
138 | jekyll-theme-primer (0.1.8)
139 | jekyll (~> 3.3)
140 | jekyll-theme-slate (0.0.4)
141 | jekyll (~> 3.3)
142 | jekyll-theme-tactile (0.0.4)
143 | jekyll (~> 3.3)
144 | jekyll-theme-time-machine (0.0.4)
145 | jekyll (~> 3.3)
146 | jekyll-titles-from-headings (0.1.5)
147 | jekyll (~> 3.3)
148 | jekyll-watch (1.5.0)
149 | listen (~> 3.0, < 3.1)
150 | jemoji (0.8.0)
151 | activesupport (~> 4.0)
152 | gemoji (~> 3.0)
153 | html-pipeline (~> 2.2)
154 | jekyll (>= 3.0)
155 | kramdown (1.13.2)
156 | liquid (3.0.6)
157 | listen (3.0.6)
158 | rb-fsevent (>= 0.9.3)
159 | rb-inotify (>= 0.9.7)
160 | mercenary (0.3.6)
161 | mini_portile2 (2.1.0)
162 | minima (2.1.1)
163 | jekyll (~> 3.3)
164 | minitest (5.10.2)
165 | multipart-post (2.0.0)
166 | net-dns (0.8.0)
167 | nokogiri (1.7.2)
168 | mini_portile2 (~> 2.1.0)
169 | octokit (4.7.0)
170 | sawyer (~> 0.8.0, >= 0.5.3)
171 | pathutil (0.14.0)
172 | forwardable-extended (~> 2.6)
173 | public_suffix (2.0.5)
174 | rb-fsevent (0.9.8)
175 | rb-inotify (0.9.8)
176 | ffi (>= 0.5.0)
177 | rouge (1.11.1)
178 | safe_yaml (1.0.4)
179 | sass (3.4.23)
180 | sawyer (0.8.1)
181 | addressable (>= 2.3.5, < 2.6)
182 | faraday (~> 0.8, < 1.0)
183 | terminal-table (1.8.0)
184 | unicode-display_width (~> 1.1, >= 1.1.1)
185 | thread_safe (0.3.6)
186 | typhoeus (0.8.0)
187 | ethon (>= 0.8.0)
188 | tzinfo (1.2.3)
189 | thread_safe (~> 0.1)
190 | unicode-display_width (1.2.1)
191 |
192 | PLATFORMS
193 | ruby
194 |
195 | DEPENDENCIES
196 | github-pages
197 | jekyll-redirect-from
198 |
199 | BUNDLED WITH
200 | 1.14.6
201 |
--------------------------------------------------------------------------------
/examples/nt-seq/test_gcContent_randomer.fa:
--------------------------------------------------------------------------------
1 | >randomer_0.0gc
2 | TTAATTAAATTTATTAAATTTTTATATTTAAAATTTTAATATTATATTAT
3 | TAAAAATTAATTATTATTATTAAAATTTTATTTAAAAATATTTTAATTTA
4 | TTTTATTAAAATTATTTAAAATAATTATTAAATTTATATATTATAAAATT
5 | TTTTATTAATTTTTTTATTATAAAAAATAATAAATTTTAATAAATAATTA
6 | TAAATAATATAAAAATTAATAATATAAATAAAAAAATAATTAATTATATT
7 | TATTTATATAATATTATTAAATAATTTTATAAAATTTTATATTATATTTA
8 | TTTATAAAATATTTTAATAATATTTATAATTTATAAAATATTTATTATTT
9 | TTAAATATATATTTTATTTAATAATTTTTTAATATATAAATATTAATTAT
10 | AAATTAAATTAAAATAATTATATAATTATAAAATTTATTATATAAATAAT
11 | AATTTAAAAAAATTATTAATTTATTAATTTATATAAAAATTTTTTATATT
12 | >randomer_0.1gc
13 | TAATTAAATATGTTTTTGTAAAATATAATAAAAACTTGTCTATTTAATAA
14 | TTTTATGACGAAAATTAAAGAGACAATAATAATTGCAAATATTATATTAT
15 | AATAATATTAAGATAAAATAACTTTGTAATTAATTATATATTTTTTTAAA
16 | CTTTATTTGATTAAATATAATAACTTTAACATATTTATAAATTATAATAA
17 | TTATATTTAAGATTGTTTATAGAAAAAATAATTCTTAAATGTTAATATAT
18 | TAATTTTTATATTAAAAATATAAATAATAGATAAGTACAAGAATACTAAA
19 | ATTAAATATATTATTCTTTTATAAAAAATATTTTAGATTATCATACTATT
20 | ATATTATTTAAATATAATATTATTTGTATTGTTCTCATCTTAATAGTTAT
21 | TATTTTTATTACGTTTTTAAATAACTAGTAATAAATATCTTTCATAAATG
22 | AAAATTTTTTTTATTAATAATTATATTAAAATGTTTTTAAATTTTTTCAT
23 | >randomer_0.2gc
24 | TCTAATAGTCTTTTTTTCTAATGACTTAACTCGTTAAGATTATAAAATTG
25 | ATTCTTTCGATAGTTAAAAATCAAAAATTCAGAATGTAAATTAAAGTATT
26 | TATCTAACAGTTTATATCTCGAATACTTAATCATTTTTTATATTCTGCGA
27 | AAATTTATACTGCTTATTCACTAAATTGCGAAATTTATACTGATATATGA
28 | ATTTAAACTAAAGCAGGACTCTTAAAATTTGGAGTTGTTAATATTTAATA
29 | TTCTAATCGGTTTTTTCATGCACTATTGCAAGTAATTGACAAGGGTTTGA
30 | CATTGAGTAACAAAACAATTTTAGGTTGAATAAAGTATTAAGAAAAATAC
31 | ATGCTTGGTATAATAAAATTAAGAAACCAATATAAAGACTACATCCTCAC
32 | TTAAATGAAAATAAACACAGAATAATAATTACTTTTTTGATACGTGAAAC
33 | ATATTCCATAGTAATTTAAAGATTTGAAAATTTATCACTTCTAGGATTCT
34 | >randomer_0.3gc
35 | TTTCTGAATATAAACGCCAAGTTGAATTCGTATTTGGAAGTACGATAAAT
36 | CAATCTGGATGAGACGTGTTTCATTTATATCGTAAGTAGGGTCGACCAAG
37 | AACCACAAGATGTAACAGTGTATAAGTAATTGTCAATAAACCATTGTGTT
38 | TTTATAATAATATCAGAATCTTTAAGTCGTGTCAATTAAACTCGGATTAC
39 | AGTATTTACTCCATCTTGTGGTTACTCACAATTTATAATTCATCTCAAGT
40 | CAAGCCATTACCTCTTTGAAATGCCGTATGAATTAATATGTATACTTTGT
41 | GCGGATTTACTATGATTTGTTTAGAATCGTTTAAAGGTACAATCAAATTC
42 | CTATTTGTATGTTCAGCTAACTTATACCCAACCCCCAAAATTTAGTAGGT
43 | TGTGAGATGTTATAGAACTTCTGGTTCATCTCGTAGGATATCAAGCTTTA
44 | TTTTAATAAAGCTTTCCATTCGAGTATAGCAGAAAAAACGCTTACTGAAT
45 | >randomer_0.4gc
46 | TGTGCAATCCTTGTACCTTAACTAAGGTAGCTACCAATATTTAGTTTTTA
47 | AGCCTTGCGACAGACTTCCTACTTAGATTGCCACACATAGAGCTAGTGAA
48 | TCAGCGAAAAGCATGACGCGCTTTCAAGCGTGGCGAATATGTGAATTAAG
49 | GCTTCGGACAGGACTATATACTTAAATTTGATCTCGCCCCGAGAACTGTA
50 | AACCTCAACATTTATAGATTATAAGATTAGCCGAAAATGCACGTGGTGGC
51 | GTCCGTCGACTGCTCCCTGAGTGTGGCTCTTTGTTCTGTCAATATCCAAC
52 | CTTTATCACGATCGATTTTTTCTACGAACCATGTTGTTCTGATACTTTGG
53 | CCATATTTCCGTTGTAGGAGTGAAATCACTTAGCTTTGCGCCGTAGTTTT
54 | AATGAAAAACCTATGGACTTTGTTTAGGGTAGCATCAGAAATCTAAACCT
55 | TCAGAAAGTGAAGATCCCGAGTATAGACCTTTATCTGCGGTTCAAGTTAA
56 | >randomer_0.5gc
57 | GCATAAGGCTGCATGCTACCTTGTCACACCTACACTGCTCGAAGTAAATA
58 | TGGGAAGCGTGCGACCTGGCTCCAGGCGTTCCGCGCCGCCACGTGTTCGT
59 | TAACTGTTGATTGGTGGCACATAAGTAATACCATGGTCCCTCAAATTCGG
60 | CTCAGTTACCTCGAGCGTTATGTCTCAAATGGCGTAGAACGGCATTGACT
61 | GTTTGACACTAGCTGGTGTTCGGTTCGGTAACGGAGAATCTGTGCGGCAA
62 | TGTCATTAATACATTTGAAACGCGCCGTACCGATGCTGAGCAAGTCAGTG
63 | CAGGCTCCCGTGTTAGGATAAGGGTAAACATACAAGTCGATAGAAGATGG
64 | GTAGGGGCCTTCAATTCATCCAACACTCTACGGCTCCTCCGAGAGCTAGT
65 | AGGGCACCCTGTAGTTGGAAGGGGAACTATTTCGTGGGGCGAGCCCATAC
66 | CGTCTCTCTTGCGGAAGACTTAACACGATAGGAAGCTGGAATAGTTTCGA
67 | >randomer_0.6gc
68 | ACGATGGTTATTAATCCTAGCGACGGAGCGCTGTCTGGAGGGCGGGTCTG
69 | ACGGAGCGCAACTCGATCGGTCGCTCGCCATTCGGACTGGGCGAAAGATC
70 | CCAGCGCTCATGCACTTGGTCCCGAGGCCTGGCCCGATATATGAGCCCAG
71 | GCTAGAGCGGGGCTGTTGACGTTCGGAGTTGAAGAAGCCCATTACACCAA
72 | TCGGCTTCAACGTGCTCCACGGCGGGCGCCTGACGAGGGGCCCACACCGA
73 | GGAAGTAGGCTGTTGCGCGCTGGGGGTAGCGGCGGCTAACCAAGGCGCCT
74 | GCCACGGCAGCAGTATCAAGCCCGTACAAAGGGAACATCCACACTCCGGT
75 | GGACCGAAGCGCGGCATCAGGGTTTCCTTTTGGATACCTGATACAAGGCC
76 | CATCGTGGCCCTTAGACTTCGCACACTTACACCCGCACCGCGCGCATGTG
77 | GAATTAGAGGCGAGGTACGATCCCTAGACCGACGTACGATGCAACTGTGT
78 | >randomer_0.7gc
79 | GGGTGCGGCGGGCCCCTCTTATACGCTCCGCCCGCCGGACCGGCCCCGGC
80 | ATGGCGCGGCGGTGCACAAGCAGATGACGACTGACCGCCGTGTATTCGTT
81 | ACGGCACCAGGCAGTTCGGGCCGGGACAATGGGGGCCGCAATGCGCAGTC
82 | TACCGCGTCCTGGCCCAACCGACGCGCTGCCATGGACGACCAGCCATGCC
83 | ACCGGCTCTCGGGCAGCCCGGTGCAGCGGTTACGAAGGGCTTGCGGGGCA
84 | TGGCCGCGGCCCGCTCAGCCACGTGCGAGGGGAGAGACCTCCGCGCATCC
85 | GTACGCTCGCCCGTCTACTACCCGCGCCCGGGGGCTACGCAGGTCGTGGG
86 | GTGCGGGGGAGGCCCTCGACCTTCCCGTGGGACGTCGACCTACCCCTTGA
87 | TAGAGCGCCCCGCTCGGGCGTGGCAGTGAGCACGCCTTCTCAGTTGTGCC
88 | AACCCTCGTCCTCACCGAAGCTTGGAGCCAATGATCAGGATCGCTGCCTC
89 | >randomer_0.8gc
90 | GCGGCAGACCCCCCGCCCACAGCCGCCCGCGCTGAGCTACCCGGCGGGCC
91 | GCCAGCCTGACCCGGTCTGTCGGGCCGCGACTACGTGGGCCGGGGCTCCG
92 | GACCGCGCCGCATAGTCGGGCCCGGCCCGGCCCCCGCGACTGCAAGCCCC
93 | AGCTTGCTCGGGTAACGTGGTTAGCCGGAGCTGCACGGGGCGCCCGCCGC
94 | GGGGTCCCCCCCGGGTGTCCCTCCCCCATCCGACGGCGGGCGGCCGCCAC
95 | CGCCGCCGACTGGTACGGGGGGCGGTGGCGCCGCCGTGGGCCCGGCACGC
96 | CACCCTCGCGGGCGTGGGGCCACCTGGCCACGCGCCGAGGTCCCACGGCG
97 | GAACCGATGGACAATGGTCCGGGCGGCACCGGGAGCCCGTGGCGCGTGCA
98 | CCCCGGCGTGGCGCGCGTGCGGCTCAACCACCGCTCCATGCCAGGGCGCC
99 | GGCTGCATGCCGGGTTGACACGCCCGCGCCGCCCGGGGAGAATATGCGAG
100 | >randomer_0.9gc
101 | GCGGGCGGCCTGGCCGGGGCGCCGCCCCGCCGGCGCGCGCTCGGGTGCCG
102 | CCGGCTGCCCGCACGTGAGCGAGGCGGCGGGGCGTCACCCCCGGCCCTCT
103 | CACCCCCGGCGGTGCGCGCGGGGCGGCGCCGGCCCGGGCTGGCTCCGCGA
104 | CGGTGCCTGCCGGCGGGTGGGGGGGCCCGGGGCCCGTCGGCCCGCGCCGC
105 | CGGGGCCACCCGGACGCCCCGCGCCGGCGCCGGGCGCGTCGGCGCGCGCC
106 | CCCCCCCCCGGAGGCGCGCGGCCGCGCGGCCGGGCGCGCGGTGCGCGCGC
107 | CCGCCCGGCGCGCCCACCTCCGCAGGCCCGGCCCGGGGGCCGGAGGGGCG
108 | CCCTCCACCCGGCCGGGCGACGCCCTGGCGGGGCGAGCCCGCGCCGCGAC
109 | CCGTGCGGCGGGGGCAAGGCCGCTGGGGGCGGGGGCGGCCCCGGACCCCG
110 | CCTACCGCTGCCGGCGAGGGGCCCCCGTCTGGGGGGCGGGTGTCGGCCGG
111 | >randomer_1.0gc
112 | CGCGGCCCGGCGGGGGGCCCGGGGGCCGGGCCGGGCCGGGCGGCCCGGCG
113 | CCGGCGCGCCCGGGGCCGGGGCGCGGCGCGGCGCGGCGGCCGGGGGCGGC
114 | CCCGGGGCGCGGGCCCCCGGGGCCGGGCGGGCCCGCCGCGGCGGCCGGCC
115 | CCGGCGGCCCGCGCGCGCGGCGCCCCGGGGGGCGCCCGCGGGGGGGGGGC
116 | CCCCCGCCGCCCGGGGCCGCCCGCGGCGGCCGGCCGCGCCCCCGGCCGCC
117 | GCGGCCGCCCCCGCGCCGGGCGGCGGGGGCGGCCGCGCCGCGGCGGCCCG
118 | GCGCGGCGCCCCGGGGCGCCGCCCCGGCGGGCGCCCGCCGGGGCCGCCGC
119 | GGGCCCCGGGCGCCGCGCGCGCGGCGCGGGGCCGCGCGCGGGCCGGGCCG
120 | CCGGGGGGCCGCGCCCCCGCGGCCGGCGCGCGGCCCGGCCCCGCCGGCGC
121 | GGCGGCGCCCCCGCCGGCGCCCCGCCCGCCGGGCCCCCCCCGCGGCGGGG
122 |
--------------------------------------------------------------------------------
/examples/nt-seq/test1.fq:
--------------------------------------------------------------------------------
1 | @SRR794330.2 HWI-ST434:134117522:C1N85ACXX:8:1101:1493:2158/1
2 | TGGCTTTGAAGAAGGAGGATGGGGCCACCAGCCAAGGAATGCAGGGAGCCTCTAGAAATTAGAAAAGGCAAGGCAACAGATTCTCCCCTAAAGCCTCCAG
3 | + comment
4 | ;=?ADDD?<4C4;CEFEGE@@7@+@C;EDB)CDDE9B@>?D9??@FA<@@FAE@=D@EEE.)=?BB75=@@1;2(5;<9?>@@B>A:@B?@@########
5 | @SRR794330.3 HWI-ST434:134117522:C1N85ACXX:8:1101:1684:2048/1
6 | ATACAAAAATTAGCTGGGCATGGTGGTGTGCACCTGTAATCCCAGCTACTTGGGAAGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGTAGAGGTTGCA
7 | +comment
8 | <@FHGHGHCFFGIIJJJIAGADFGGIFHD@DDGHEICGA@FFAHGECC>CD?@;>AC@A??AABC2???@@2>@CC?:?CB@
9 | @SRR794330.4 HWI-ST434:134117522:C1N85ACXX:8:1101:1621:2117/1
10 | GACAGGCCAGTTCTCTCTGTGTATATTCTAGGTTTTGAGAAATCACAACCAGAGCCCCCTGGCTCCACGTCCACCATGGTTTTTCCCTTGAATGGTGCTC
11 | +
12 | =E@HGIII+ACHHIGC?=BABDBG@FFBG((=.@CAA=BEB?A;;@CC@CBBBCCCCC9A:@>>C>>>>
13 | @SRR794330.5 HWI-ST434:134117522:C1N85ACXX:8:1101:1575:2184/1
14 | TTTGTAGGAGGATAATAAGACTATGCAAAGTGTCTAGCAGAGTGAATGACCCATAACAAACTCTCAGTAAATGTATTACTGTAACAGCCTATTGAATAGA
15 | +
16 | ??@BDDDDC##
17 | @SRR794330.6 HWI-ST434:134117522:C1N85ACXX:8:1101:1743:2228/1
18 | ATTTTGGAATAAATATGCCTTTGTCGTGGGAGTCTGTCAGGTGTGTTCTAGGATGTTTAGCAGCATTGCTGGCCTCTACGCACTAGATGTTAGTAGCAAT
19 | +
20 | +:?+AA8;:CFFFIFFF>FE99;FF@BF@FF@FFA4B8B4B))=)(6@==.>7==.7;?B>(3=/9;;;@A###########
21 | @SRR794330.8 HWI-ST434:134117522:C1N85ACXX:8:1101:1922:2069/1
22 | TGAAAGGATAAAAGACAAAAATTACATGATTATCTCAGTATATGAAGAAAAGGCATCTGATTAACTCCAACACCCTTTCATTGTGAACACAATCAGCAAA
23 | +
24 | @?;DDD?;FFDFDEGHIIIEGIIIGIIGIIIIIFDHDED@C?GBFDFFHAHA;F9BDDFDDCB.BFH;8=F=ED===AHFFFB@@E<@CEC?CC>;A:55
25 | @SRR794330.9 HWI-ST434:134117522:C1N85ACXX:8:1101:1888:2078/1
26 | AGGAAACTTACAATCATGGCGGATGGTGAAGGTGAGGCATGCGTGTTTTACCATGGTGGAGCAGGAGACAGGAAACAAAGAAGGATGTGCTACACACTTC
27 | +
28 | @@?DDGAGHGIB7==AEE7=?9B@C@AAB?BC?<@B?>CBBCCBAC>CCAC:@CCBCC:
29 | @SRR794330.10 HWI-ST434:134117522:C1N85ACXX:8:1101:1833:2100/1
30 | ATTCCTCAGGGTCATTGCCCTAGACTGAGTGTAGCATGATTGGACCATCTGAGAAGATGGTGGGATAACAGAAAGTTATTTGGAGTCTTCAGACCTCAGT
31 | +
32 | @@CFFFFFHHHFHHIJJIJJJIJJJIIIJFHHGIJJJJJJIJJIHJIIJJJIJJIJJJIJBFIIIFEGIGHIHHHHHHFFFFFFECECDEEDDDDDDDDC
33 | @SRR794330.11 HWI-ST434:134117522:C1N85ACXX:8:1101:1929:2152/1
34 | TGAAACCCTATACTCACTTTGTGCAATCCTTTGGTAAGTGCAAAGTGAGAACACAGGTCTGATATGTACAAGTTTCAGTGAACATGGTACTATGCATCAT
35 | +
36 | @B@FFDDDHGHHHJHEHGIJIHIHCHJIJJIHIJFEGIFHIGEGFGICDHHIFICHEEGIHGIGHIHGHGGIHIJJGHGHHGHGHFFECEFFFEDDD>@C
37 | @SRR794330.12 HWI-ST434:134117522:C1N85ACXX:8:1101:1977:2153/1
38 | ATATGAGAATGACAACAATGGATGAAAGGCCTCAGCTTTAGAGTCAAGCTGAACAGTTTGAAATCTGTATTTGACATTTACTAATGTGATCTTGCACAAG
39 | +
40 | @C@DFFFFGHGHHGIHIJGIJIJGDGGHHDIIIHJJIIIIGIIGGHFGHIHIEHGHFFFEDHJIJJJEGHIJIDIEHGIFHHHGHEBEFFFFFEEEEEDD
41 | @SRR794330.13 HWI-ST434:134117522:C1N85ACXX:8:1101:1996:2237/1
42 | GACTCAGCCTTTTCTGACACCACCCTGAAGGGAGCATTAAGGTGAGCTGTTGTAACTTGTCAACAGTGGAAGTCTGTTTTTGGTGGTGCGTATCTATTCA
43 | +
44 | @@@FFFFFFFHGHIJCHIGEIIJJJJ>GGABBDB?CD7<?CB?B?8@CCCC<4C<<8<<
49 | @SRR794330.15 HWI-ST434:134117522:C1N85ACXX:8:1101:2050:2058/1
50 | CCACCGCACTGTGCCTTTCCACAATCATCTTCCCACCCGGGGCCACCACACTGTGCCTTTCCACAATCATACTTCTACCCAGGGCCACCACACTGTGCCT
51 | +
52 | @@@FDFDDDDHDHIIIIIIHHIGGHHHGHGGHHIJIGGGBGIGGIIGHGHFFE?DC@ACECAACC@CDCC(5>CC>AC(5:?79(<<<C>CBDBACDDDDA
57 | @SRR794330.17 HWI-ST434:134117522:C1N85ACXX:8:1101:2190:2103/1
58 | CCATACCATTCCATTCCATTCCATTCCATTCCGTTCCATTCCGTTCCATTCCATTCCATTCCATTCCATTCGAATTAATTCCATTCCATTCCATTCCATT
59 | +
60 | C@CFFEDDHHHHHJJIJJJJJJJJJJJJIIJJJIJIJIJJJJJGIJIJHIJIIJJGIHJJHIJJJJJJJJJIJJJIIIJIJJJJJJJJGJJGIIJJIJJJ
61 | @SRR794330.18 HWI-ST434:134117522:C1N85ACXX:8:1101:2159:2122/1
62 | CTCTGAACAAGGAAAACATGAAGGCAAAAACAAAGATAAAATACAGTTAAAAATGCAGTGGCTGACTGAAAAATGTATGCCACAAGGAACACAGAGCACA
63 | +
64 | @C@FFFDFBHHGGIIIJJIGIGJGGHJJIJGGIJIFIIJIJJEHIIDFGIJGEIIEGGBCAEGIHEHDIHHFHHFFDEFBCCEBCEDDCDDCDBACCC?C
65 | @SRR794330.19 HWI-ST434:134117522:C1N85ACXX:8:1101:2244:2122/1
66 | CCTCACCCTGTTGACATAGTATGATAGAATGTGTAACCACTTAATCTACCTTAAGATGCTATTGGGCAACAACAATGTCTTGACTTTAGGGGCTGGAAAG
67 | +
68 | CCCFFFFFHHHHHJJJJJJJHIJJJIJJJJJJJIJIIJJJJJJJJJIIJJJJJJJJJJJJJJJIIJJIJIJJJJJIJHHHHHHFFFFFFFEDDDDDBDDD
69 | @SRR794330.20 HWI-ST434:134117522:C1N85ACXX:8:1101:2012:2162/1
70 | GCCTGTTCTTTCCACTAAATGAAACAACCTTAATAAAAATGCTGTTCTTACAACTTCAATAAGAGCTTTTGTCTTACATTAAAGCTTTATAATATTGCAT
71 | +
72 | @@@FFFFFHGHDHIJIJJJIIIIIJJJGIJJJJIJFIJJIIJJJGEHGIGHIIJIIJJJJJJJJJGJIJJJJJJIEHHIJHHGHHHFFFFFFFEEFEDDE
73 | @SRR794330.21 HWI-ST434:134117522:C1N85ACXX:8:1101:2062:2165/1
74 | CCCAGGCTAACAAATGTCTATCAGGTACCCAACACAAAAACTAAAATCTTCTCAGGAAACCCTTAGACCTCAAATTATTCCTAGAAATAGCTTTTCCAAC
75 | +
76 | CCCFFFFFHHHHHJJJIJJJJJJJJJIJJJJIJJJJJJJJJJIJJJIFHHIJJJJJJJJFHIJJJJJJJJHHHHHFFFFFFFEEEEEEECCDDDCCDEDD
77 | @SRR794330.22 HWI-ST434:134117522:C1N85ACXX:8:1101:2148:2195/1
78 | AAACAATTTTTTAATTGTGAAAAGATTCTTGATAACACGTTTCCTATGTGCATCCCTTTAAGGCAATACAGTTTGGATTCTGGAAATACTGGTGGAAAAA
79 | +
80 | @CCDFFFFHHHHGJJJJHJJIIIIIJJJJJJIJJJJJIJGHJJJJJJJIJJJIIJJJJJII@GIIIJIJIIGHHHHHFFFFFFCEEECEEEDCCDBDDDB
81 | @SRR794330.23 HWI-ST434:134117522:C1N85ACXX:8:1101:2026:2224/1
82 | TCAGTACTTTGAAAAGCTCCCAAGTGCTTCTTGTGATGCATCGGGTTTGGGATCTTCTGCCCCAGGGAGCGCTTCCCGATTACTTCATATCTAATCCTCA
83 | +
84 | ?;?DB>DDDDADD>@??8,8?>>>(54>(:>B>:A>:A>
85 | @SRR794330.24 HWI-ST434:134117522:C1N85ACXX:8:1101:2191:2246/1
86 | CCCTTTACTCTTGGACATTCAGTTTAGTACATTTCTCTTCCTCCCTGGCAATAGGATGTGGCCTTGTACCTGAGTTCTGGTCATTGAAATATACATCTGA
87 | +
88 | CCCFFFFFHHHHHJJJIJJJJJIJJJJHGIJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJIJJJJJJHEHIJJHHGGHHFFFFFFFEDEEEEE
89 | @SRR794330.25 HWI-ST434:134117522:C1N85ACXX:8:1101:2426:2041/1
90 | TGTGCTCACACCCAGAAGATGGCCATGTGGTTTGCCCATCCACCAGAATGGATGCTCTGGGTACTCTTTGAGCCAGCTTGGCCTTGCCTAGCATGCACAG
91 | +
92 | @@BDFFFFHHHHHJ@GHJIJJJJJJJJHHJFHHGJJJJJJJJJJEHHJDGGHGHIIIDHIFHIIJJJJHFHHFFF@DBEDDEEDDDDDDDDDDEDDDDDD
93 | @SRR794330.26 HWI-ST434:134117522:C1N85ACXX:8:1101:2337:2087/1
94 | AAAGATAACTTTGGTTTTTTCACTTGTAAAATGGAGATAATAAAAGTATATCACAGAGTCATTATGCAGATGAAATGAATTAATATATGAGATCGGAAGA
95 | +
96 | C@@FFFFFHGHHGJEGIIJJJJJIIJGGIJJIJJIJIIJJJIJJJJDGGGIIEGIIJGFGEGIGGIJIIIIHIGIHHHHEHHFFFFFFFEEECECDBDDD
97 | @SRR794330.27 HWI-ST434:134117522:C1N85ACXX:8:1101:2490:2107/1
98 | TATTTTATTGAGGATTTTCGCATCAATGTTTATCAGGGATATTGGTCTAAAATTCTCTTTTTTTGTTGTGTCTCTGCCAGGCTTTGGTATCAGGATGATG
99 | +
100 | CCCFFFFFHHHHHIJJJJJJJJJJJJJJIJJIJJJJJJHHIIJJJGHIJJJJJJJIJJJJJJJJHHHHFFFFEECEEEDDDDDDDDDBDDDEEDDDDDED
101 |
--------------------------------------------------------------------------------
/syntax/less/sam.lang:
--------------------------------------------------------------------------------
1 | # Sam language definition file for less pipe
2 | # bioSyntax v0.1
3 | # Depends on sam.style + bioSyntax.outlang
4 |
5 | # Variables ----------------------------------
6 | vardef NUCLEOTIDE = '[ATCGNXatcgnxRYSWKM]'
7 | vardef PHRED = '[!-K]' #PHRED 1.8
8 |
9 | # Header-section -----------------------------
10 | environment header start '^(?=@)' begin
11 |
12 | # Standard Headers HD | SQ | PG
13 | environment header_hd delim '(?=@(HD|SQ|PG))' '$' begin
14 | header = '@[HSPC][DQGO]'
15 |
16 | #HD
17 | numeric = '(?<=VN:)\S*'
18 | mal = '(?<=SO:)(unsorted|unknown)'
19 | bon = '(?<=SO:)(coordinate|queryname)'
20 | mal = '(?<=SO:)\S*'
21 |
22 | mal = '(?<=GO:)(none|)'
23 | bon = '(?<=GO:)(query|reference)'
24 | mal = '(?<=GO:)\S*'
25 |
26 | #SQ
27 | chr = '(?<=SN:)\S*'
28 | chrStart = '(?<=LN:)\S*'
29 | chr = '(?<=AH:)\S*'
30 | chr = '(?<=AN:)\S*'
31 | chr = '(?<=AS:)\S*'
32 | string = '(?<=M5:)\S*'
33 | chr = '(?<=SP:)\S*'
34 | numeric = '(?<=UR:)\S*'
35 |
36 | #PG
37 | software = '(?<=ID:)\S*'
38 | software = '(?<=PN:)\S*'
39 | commandline = '(?<=CL:)[\S ]*'
40 |
41 | software = '(?<=PP:)\S*'
42 | string = '(?<=DS:)\S*'
43 | #numeric = '(?<=VN:)\S*'
44 | end
45 |
46 | # Readgroup Header
47 | environment header_co delim '(?=@RG)' '$' begin
48 | header = '@RG'
49 |
50 | sample = '(?<=ID:)\S*'
51 | string = '(?<=CN:)\S*'
52 | string = '(?<=DS:)\S*'
53 | numeric = '(?<=DT:)\S*'
54 | string = '(?<=FO:)\S*'
55 | string = '(?<=KS:)\S*'
56 | sample = '(?<=LB:)\S*'
57 | software = '(?<=PG:)\S*'
58 | numeric = '(?<=PI:)\S*'
59 | string = '(?<=PL:)\S*'
60 | string = '(?<=PM:)\S*'
61 | string = '(?<=PU:)\S*'
62 | sample = '(?<=SM:)\S*'
63 |
64 | end
65 |
66 | # Comment Header
67 | environment header_co delim '(?=@CO)' '$' begin
68 | header = '@CO'
69 | comment = '.*'
70 |
71 | end
72 |
73 | end #Header
74 | # -------------------------------------------
75 | # align-section -----------------------------
76 |
77 | environment align start '(?=^[^$])' begin
78 | drop = '$' exitall # stops multi-line searching
79 |
80 | # Column 1: CHROM
81 | string = '^\S+'
82 |
83 | # Column 2: FLAG
84 | environment push2 = '\t?' begin
85 | drop = '(?=$)' exitall
86 | # Read Flag
87 | # If flag > 512
88 | # read is QC-fail | PCRdup | 2'
89 |
90 | numeric = '\A[0-9]{1,2}(?=\t)'
91 | numeric = '\A[1-4][0-9]{1,2}(?=\t)'
92 | numeric = '\A[5][0][0-9](?=\t)'
93 | numeric = '\A[5][1][01](?=\t)'
94 |
95 | # Flag
96 | string = '\d+'
97 |
98 | # Column 3: RNAME
99 | environment push3 = '\t?' begin
100 | drop = '(?=$)' exitall
101 |
102 | chr = '\A\w+'
103 |
104 | # Column 4: POSition
105 | environment push4 = '\t?' begin
106 | drop = '(?=$)' exitall
107 |
108 | chrStart = '\A\d+'
109 |
110 | # Column 5: MAPQuality
111 | environment push5 = '\t?' begin
112 | drop = '(?=$)' exitall
113 |
114 | # MAPQ Scale (-log10 P)
115 | # Incriment size = 10
116 |
117 | gradbw1 = '\A255(?=\t)' # MAPQ NA
118 |
119 | gradbw1 = '\A[0-9](?=\t)'
120 | grasbw6 = '\A[1][0-9]'
121 | gradbw8 = '\A[2][0-9]'
122 | gradbw10 = '\A[3][0-9]'
123 | gradbw10i = '\A[4-9][0-9]'
124 |
125 | gradbw1 = '\A\d+'
126 |
127 | # Column 6: CIGAR string
128 | environment push6 = '\t?' begin
129 | drop = '(?=$)' exitall
130 |
131 |
132 | # CIGAR Strings
133 | # M: Alignment match
134 | # I: Insertion
135 | # D: Deletion
136 | # N: Skipped region (intron)
137 | # S: Soft Clip
138 | # H: Hard Clip
139 | # P: Padding
140 | # =: Sequence Match
141 | # X: Sequence Mismatch
142 | # *: String Absent
143 |
144 | clip = '\A\d++[NSHP]' # clips
145 | default = '\A\d++[M=]' # match
146 | mismatch = '\A\d++[X]' # mismatch
147 | insertion = '\A\d++[I]' # insertion
148 | deletion = '\A\d++[D]' # deletion
149 |
150 | comment = '\A\S++' # else
151 |
152 |
153 | # Column 7: RNEXT & PNEXT
154 | environment push7 = '\t?' begin
155 | drop = '(?=$)' exitall
156 |
157 | # Match Chromosome
158 | chrStart = '\A=\t\d+\t'
159 |
160 | # Unmapped Rnext
161 | string = '\A\\*\t\d+\t'
162 |
163 | # Different Chromosome Rnext
164 | string = '\A\S+\t\d+\t'
165 |
166 | # Column 8: TLEN
167 | environment push8 = '(?=\d)' begin
168 | drop = '(?=$)' exitall
169 |
170 | numeric = '\d+'
171 |
172 | # Column 9: Sequence Data
173 | environment push9 = '\t?' begin
174 | drop = '(?=$)' exitall
175 |
176 | ntA = '\A[Aa]++'
177 | ntT = '\A[TtUu]++'
178 | ntG = '\A[Gg]++'
179 | ntC = '\A[Cc]++'
180 | ntN = '\A[NnXx]++'
181 | ntN = '\A[RrYySsWwKkMm]++'
182 |
183 | # Column 10: PHRED
184 | environment push10 = '\t?' begin
185 | drop = '(?=$)' exitall
186 |
187 | # Illumina 1.8 Scale
188 | # !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJ...j
189 | # | | | | | | | | | |...
190 | gradbw1 = '\A[!-%]++'
191 | gradbw3 = '\A[!-(]++'
192 | gradbw6 = '\A[)-0]++'
193 | gradbw8 = '\A[1-8]++'
194 | gradbw10 = '\A[9-@]++'
195 | gradbw10b = '\A[A-D]++'
196 | gradbw10i = '\A[E-j]++'
197 |
198 | # Column 11+ Tags
199 | environment push11 = '\t' begin
200 | drop = '(?=$)' exitall
201 |
202 | # AB:i:1337
203 | # A Printable
204 | # i signed integer
205 | # f floating point
206 | # Z string with spaces
207 | # H byte array hex
208 | # B Integer/Numeric Array
209 |
210 | string = '[A-Z]{2}:'
211 | (comment,numeric) = `([ifH]:)(\S*)`
212 | (comment,keyword) = `([AZB]:)(\S*)`
213 |
214 | end #col11+
215 | end #col10
216 | end #col9
217 | end #col8
218 | end #col7
219 | end #col6
220 | end # col5
221 | end # col4
222 | end # col3
223 | end # col2
224 | end # align section
225 |
--------------------------------------------------------------------------------
/examples/sam/mario.sam:
--------------------------------------------------------------------------------
1 | @HD VN:1.0 SO:coordinate
2 | @SQ SN:chr13 LN:1023550
3 | @RG ID:MARIO LB:PLUMBERS SM:HG008BIT PL:ILLUMINA PU:SNES-ST64
4 | @PG ID:bowtie2 PN:bowtie2 VN:2.2.6 CL:"/usr/bin/bowtie2-align-s -8bit -1 inpipe1 -2 inpipe2"
5 | SNES1993.19247142 163 chr13 10001 22 67S34M = 10044 168 AAAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCAAAAAAAGGGGGGGGGGGGGAAAA @@?DDD:ADFHHHHIJ@ECHEIIHIJGIIIJIJIIE@BGEGIHGF<=ABD;8;;B8@@BBDBB?(8(8@@AB?BB<A???39><<59955(8;BB@BD7BD;-5-2>9B7<<@BBDB@B5-288?>@DCCDDDDD?@B7;983>>ACC>CCDD?@@BD############# YT:Z:UP RG:Z:SNES1993
9 | SNES1993.32192276 133 chr13 10001 0 * = 10001 0 AAAAAAAAAAAAAAAATTTTTTTTTTTTTGGGGGGGTTTTTGGGGAAAATTTTTTTTTTTTAAAA ?8:=+B:BACA35(9/;B><<9;;@8;@B;;;08A8(9>+99???@# YT:Z:UP RG:Z:SNES1993
11 | SNES1993.35553638 69 chr13 10001 0 * = 10001 0 AAAAAAAAAAAATTTTGGGGTTTTGGGGGGGGGGGGTTTTTGGGGGGGGGGGGTTTTTTTTAAAA BBCFFFFFGHHHHIIIGJJJJJGHIFGGGHHHIJJJJHGIHGGHHGJHHHHH@CDACDDDDDDDDDABBDBBDA@@CCCDB9>09:DBBDBDDDB@@<B<@DDDCCC<9BBA;5D@AC@<@@DDDDDB?DBBDBDDDDBD@=BDHGHGJIHEFB<.GHGEGIHIHGGIHHHHFFDEFFFCCB AS:i:65 XN:i:0 XM:i:3
15 | SNES1993.32192276 89 chr13 10001 22 67S34M = 10001 0 AAAAAAAAAAAATTTTTTTTGGGGGGGGGGGGGGGGTTTTTTTTTTTTTTTTTTTTTAAAAAAAA #######AAAB44+()(>ABA>4<<3;>>>>903AA><=3?>A>8/88>????A?9'6=?C;DCDIDIDDDD6BDDDB)@IIDDE?8@AD@:DBBDBA:;=BB@9FFEEGBA@GF@/;@CB?BBBB2(82+43:C:93<<9@0-<1:>+9@C(9?## YT:Z:UP RG:Z:SNES1993
19 | SNES1993.7932405 1177 chr13 10003 36 101M = 10003 0 AAAAAAAATTTTTTTTTTTTTTTTCCCCTTTTTTTTTTTTTCCCTTTTTTTTAAAAAAAAATTAA ############?90&B<9DDBA>DC8+B@??<2&+0<3BB@BD@2DB?CABACDC@@A??BCDFFFHE<@8AHHFEDBCC>C>C95@3AA>?A@DFFDEDC;)EHEE;JIIH@AIEIGFD:GGGEIJIIIJJIJJGHEHF@6?661@0730706@9)58<2323:ACB########################################### AS:i:198 XN:i:0 XM:i:1
22 | SNES1993.58751284 99 chr13 10143 36 101M = 10352 234 GGGGGGGGTTTTTTTTTTTTTTTTTTTTCCCCTTTTTTTTTTTTCCCCAAAAAAAAATTTTTTAA @CCFFFDDHHHHHIJJJJJJIJJIJJFBBDBDBDDDDBDBBBBDDDDDCBCCDDDDDBDBB@BBDD@@B>B?CCCCD58?@BC8>>B59CC?>:<@898@A559B(8<08<5;7;5A3>C3::;8?########################### AS:i:198 XN:i:0 XM:i:1
24 | SNES1993.57860057 73 chr13 10149 44 101M = 10149 0 GGGGGGGGGGGGTTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCGGGGCCCCCCCCCTTTTTTAA BCBFFDDFGHHHGJIJJJJJJIIEHFFC8@D@D@@DB@1BB??ACCCDDD@BD????ABBBB@BD3@C(:@@?@>AA(55<99+9AC>BDD<9AC?##### AS:i:195 XN:i:0 XM:i:1
25 | SNES1993.57860057 133 chr13 10149 0 * = 10149 0 AAAAGGGGAAAAAAAAAAAATTTTCCCCCCCCGGGGCCCCCCCCCCCCCCCCCCCCCTTTTTTAA @C@DFFFFHGHHHIJJIJJGJIDHIJGBHIGIGF9>;=A;ACD?AC?A?A@AC>@<<:AABBDB5?CDC>AB9?AC@>?BB&)2(3>AACACACB YT:Z:UP RG:Z:SNES1993
26 | SNES1993.2803200 73 chr13 10151 44 100M1S = 10151 0 AAAAGGGGAAAAAAAAAAAATTTTCCCCCCCCGGGGCCCCCCCCCCCCCCCCCCCCCTTTTTTAA 7@?:ADDDFDFDD6:EAF6B/;AABB/9?6/3093900-2<<>A8ABB<07@<0(28&)77@?###################################### AS:i:196 XN:i:0 XM:i:1
27 | SNES1993.2803200 537 chr13 10151 0 * * 0 0 AAAAAAAAATTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTTTTTAA ?@??;DDDA1@FDDEAEHIDC4))807;'51A=>66<:5,(,308?CD##################################################### YT:Z:UP RG:Z:SNES1993
28 | SNES1993.9345310 137 chr13 10152 44 101M * 0 0 AAAAAAAAATTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCTTTTTTAA BD/=@B66:6:B5399><5 AS:i:202 XN:i:0 XM:i:0
29 | SNES1993.9927629 73 chr13 10152 44 100M1S = 10152 0 AAAATTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA @@?DDDDDFFHFHI:F@F6BHD:/?>@?/;;7@0&65@######### AS:i:194 XN:i:0 XM:i:1
30 | SNES1993.56664346 137 chr13 10152 44 101M = 10152 0 AAAATTTTTTTTTTTTCCCCCCCCCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAAAAAAAAAA @@CBD@D8>BBD@B5@### YT:Z:UP RG:Z:SNES1993
32 | SNES1993.9927629 133 chr13 10152 0 * = 10152 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ?1:ADDFF6D60?8).)=.=F@623=@>>;C6<3'(;??BB8?B@DB&002830&&823<@B758)0(59;@><@><@C(:34(95-50(:>3599B@A@C YT:Z:UP RG:Z:SNES1993
33 | SNES1993.56664346 69 chr13 10152 0 * chr2 2001337 0 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA ??@DDBD:@DDHHBC>?CEDHGHFHEAFGE@:C@BDGIGGG'@BE=E>A#################################################### YT:Z:UP RG:Z:SNES1993
34 | SNES1993.26275897 99 chr13 10153 44 101M = 10238 186 GACCCCCGAGCTGTGCTGCTCGCGGCCGCCACCGCCGGGCCCCGGCCGTCCCTGGCTCCCCTCCT CCCFFFFFGHHHGJGIJJJJIJHFDDDDDDDDBBBDDDCBCD>CDBBDDBBA99>CCCC@>?BBD?CCDDBBBB#### AS:i:202 XN:i:0 XM:i:0
35 |
--------------------------------------------------------------------------------
](assets/images/sam-less.png)
--------------------------------------------------------------------------------
/syntax/less/flagstat.lang:
--------------------------------------------------------------------------------
1 | # Flagstat (.flagstat) language definition file for less pipe
2 | # bioSyntax v0.1
3 | # Depends on sam.style + bioSyntax.outlang
4 |
5 | # QC-Passed Reads
6 | numeric = 'QC-passed reads'
7 | numeric = '^\d+'
8 | numeric = '\([\d\.]+%'
9 | numeric = '\(\-?nan%'
10 |
11 | #QC-Failed Reads
12 | keyword = 'QC-failed reads'
13 | keyword = '(?<=\+ )\d+'
14 | keyword = '\:[\d\.]+%'
15 | keyword = '\:\-?nan%'
16 |
17 | #string = 'mapQ'
18 |
--------------------------------------------------------------------------------
/syntax/less/fasta.style:
--------------------------------------------------------------------------------
1 | // Fasta Style File -- less
2 | // bioSyntax v0.1
3 |
4 | // Header
5 | header black b ;
6 | comment gray i ;
7 |
8 | // Nucleotide Coloring
9 | ntA darkgreen ;
10 | ntC darkred ;
11 | ntG brown ;
12 | ntT darkblue ;
13 | ntU blue i ;
14 | ntN gray ;
15 |
16 | // PHRED Score Gradient
17 | gradbw1 teal ;
18 | gradbw3 teal b ;
19 | gradbw6 pink ;
20 | gradbw8 orange ;
21 | gradbw10 brightorange ;
22 | gradbw10b brightgreen b ;
23 | gradbw10i brightgreen i ;
--------------------------------------------------------------------------------
/syntax/vim/quickInstall_unix.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | #
3 | #
4 |
5 | # Detect if the line 'syntax enable'
6 | # exists in ~/.vimrc
7 | # TRUE: do nothing
8 | # FALSE: add that line to .vimrc (or replace 'syntax disable')
9 |
10 | # Change permissions to read-only
11 | chmod 0644 *.vim
12 | chmod 0644 ftdetect/*.vim
13 | chmod 0644 colors/*.vim
14 |
15 |
16 | # Copy over bioSyntax files to local vim directory
17 | cp *.vim ~/.vim/syntax/
18 | cp ftdetect/* ~/.vim/ftdetect/
19 | cp colors/* ~/.vim/colors/
20 |
--------------------------------------------------------------------------------
/syntax/less/quickInstall.sh:
--------------------------------------------------------------------------------
1 | #!/bin/bash
2 | #
3 | # Quick installer for less syntax
4 | # for testing purposes
5 |
6 | SRCDIR='/usr/share/source-highlight'
7 |
8 | # Copy over src-hilite script
9 | sudo cp src-hilite-lesspipe_BIO.sh $SRCDIR/src-hilite-lesspipe.sh
10 |
11 |
12 | # Copy over language files
13 | sudo cp *.lang $SRCDIR/
14 |
15 | # Copy over syle files
16 | sudo cp *.style $SRCDIR/
17 |
18 | # Copy over language files
19 | sudo cp bioSyntax.outlang $SRCDIR/
20 | sudo cp bioSyntax-vcf.outlang $SRCDIR/
21 |
22 |
23 |
24 |
--------------------------------------------------------------------------------
/examples/nt-seq/test1_prot.faa:
--------------------------------------------------------------------------------
1 | >PHOKE_DN21123
2 | VP*FPACNPRRHIIRSSIFS*FF*KNIFFNPKRRIIAINFFLFI*DVQTFSNLEDSPQTL
3 | THVRKKIKSSLRI*CSVLKLTDVE*KRPFRQLNYKFFQA*CTLFF*YVFKINLIIPVILP
4 | EPIYNDILTIFGIGFQLSVQR*CFRRKPSRFKLSQSTV*FVLQFYMFVTLSSKVQKMS*Q
5 | LSTHS**ATYPYFQPMAQLRGGFRVILSRTRKIGT
6 | >PHOKE_DN21456
7 | VFISFKNIRTLALQQVINKFYLY**KIRFLKNKGL*NEIV**IHTCKRYESKQYIYFLF*
8 | NAILIYNE*MRLAPL*NSTVY*QSTDLPTEIKLSLR*NLSYISTIC*VICQNQSS*ITDG
9 | NKFRNQIHKS*FQLFFFQDHMMEITGDKINEGQSYADGPCGDRKHYQILNARGSEYVENT
10 | GHNFQIHNR*SILINDFIFKKSNLYSLSEIIFLICMRNIK*YLQIVIFKVLNVSYKHRKV
11 | KKHKETFK*FKDGYIISTYHFKLAFHINFTCTDLHI*EFVNIFYQSQSGQSAELSP*HTP
12 | EV*LSHDI*YIKK*LSNCNIPTL*
13 |
--------------------------------------------------------------------------------
/syntax/vim/fasta.vim:
--------------------------------------------------------------------------------
1 | if exists("syntax_on")
2 | syntax reset
3 | colorscheme bioSyntax
4 | set nowrap
5 | endif
6 |
7 | " In the future, implement 'context-aware' fasta
8 | " in which Nucleotides vs. Amino Acid sequences are detected
9 | " and colored accordingly
10 |
11 | syntax match headerbw ">.*$"
12 | syntax match ntA "[Aa]"
13 | syntax match ntG "[Gg]"
14 | syntax match ntC "[Cc]"
15 | syntax match ntT "[Tt]"
16 | syntax match ntU "[Uu]"
17 | syntax match ntR "[Rr]"
18 | syntax match ntY "[Yy]"
19 | syntax match ntS "[Ss]"
20 | syntax match ntW "[Ww]"
21 | syntax match ntM "[Mm]"
22 | syntax match ntK "[Kk]"
23 | syntax match ntD "[Dd]"
24 | syntax match ntB "[Bb]"
25 | syntax match ntV "[Vv]"
26 | syntax match ntH "[Hh]"
27 | syntax match ntN "[Nn]"
28 | syntax match ntGap "[/\-/\.]"
29 |
--------------------------------------------------------------------------------
/syntax/sublime/flagstat.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Flagstat syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: flagstat
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [flagstat]
9 | scope: text.flagstat
10 |
11 | contexts:
12 | main:
13 | # Match Keywords
14 | - match: 'mapQ'
15 | scope: string
16 |
17 | - match: '[\\+\\>\\=\\%\\:]'
18 | scope: keyword3
19 |
20 | # Match numbers
21 | - match: '-nan'
22 | scope: numeric
23 | - match: '^[0-9]*\b'
24 | scope: numeric
25 | - match: '[0-9]*'
26 | scope: numeric
27 |
28 | # Match Descriptor
29 | - match: '\b[A-Za-z]+[12]*\b'
30 | scope: string
31 |
32 | # Match Brackets
33 | - match: '[()]'
34 | scope: comment
--------------------------------------------------------------------------------
/docs/collaborate.md:
--------------------------------------------------------------------------------
1 | # Collaborate on bioSyntax
2 |
3 | bioSyntax is a community project for biological syntax highlighting. If you work with a particular file format you'd like syntax highlighting for, develop the syntax files and we'll add them. Don't worry we can help : )
4 |
5 | ## Report a bug
6 |
7 | ## Developing bioSyntax for `.XXX` file format
8 |
9 | ## Creating a custom theme
10 |
11 | ## Other ways to help
12 |
13 | Right now check out the [bioSyntax Repo](https://github.com/ababaian/bioSyntax) and look under 'issues' for development instructions.
14 |
15 | If you're really keen, check out the [TODO](https://github.com/ababaian/bioSyntax/issues) for ways to help develop bioSyntax.
16 |
17 | [ under construction ]
18 | - How To Instructions for each program (take from issues)
19 | - Other ways to contribute...
--------------------------------------------------------------------------------
/examples/nt-seq/test1.fa:
--------------------------------------------------------------------------------
1 | >seq1_head
2 | GCTGACACGCTGTCCTCTGGCGACCTGTCGTCGGAGAGGTTGGGCCTCCG
3 | GATGCGCGCGGGGCTCTGGCCTCACGGTGACCGGCTAGCCGGCCGCGCTC
4 | CTGCCTTGAGCCGCCTGCCGCGGCCCGCGGGCCTGCTGTTCTCTCGCGCG
5 | TCCGAGCGTCCCGACTCCCGGTGCCGGCCCGGGTCCGGGTCTCTGACCCA
6 | CCCGGGGGCGGCGGGGAAGGCGGCGAGGGCCACCGTGCCCCGTGCGCTCT
7 | CCGCTGCGGGCGCCCGGGGCGCCGCACAACCCCACCCGCTGGCTCCGTGC
8 | CGTGCGTGTCAGGCGTTCTCGTCTCCGCGGGGTTGTCCGCCGCCCCTTCC
9 | CCGGAGTGGGGGGTGGCCGGAGCCGATCGGCTCGCTGGCCGGCCGGCCTC
10 | CGCTCCCGGGGGGCTCTTCGATCGATGTGGTGACGTCGTGCTCTCCCGGG
11 | >seq2_tail:1234
12 | GTTTGGGAGCCGCGGAGGCGCCGCGCCGAGCCGGGCCCCGTGGCCCGCCG
13 | GTCCCCGTCCCGGGGGTTGGCCGCGCGGCGCGGTGGGGGGCCACCCGGGG
14 | TCCCGGCCCTCGCGCGTCCTTCCTCCTCGCTCCTCCGCACGGGTCGACCG
15 | ACGAACCGCGGGTGGCGGGCGGCGGGCGGCGAGCCCCACGGGCGTCCCCG
16 | CACCCGGCCGACCTCCGCTCGCGACCTCTCCTCGGTCGGGCCTCCGGGGT
17 | CGACCGCCTGCGCNNNXnGGCGTGAGACTCAGCG---TCTCGCCGTGTCC
18 |
--------------------------------------------------------------------------------
/syntax/less/sam.style:
--------------------------------------------------------------------------------
1 | // SAM Style File -- less
2 | // bioSyntax v0.1
3 |
4 | // Header ID
5 | header black b ;
6 |
7 | // Nucleotide Coloring
8 | ntA darkgreen ;
9 | ntC darkred ;
10 | ntG brown ;
11 | ntT darkblue ;
12 | ntN gray ;
13 |
14 | // Switch (Good / Bad)
15 | bon darkblue ;
16 | mal darkred ;
17 |
18 | // CIGAR String
19 | // match default ;
20 | mismatch red ;
21 | clip gray i ;
22 | deletion yellow ;
23 | insertion purple ;
24 |
25 | // Class
26 | numeric blue ;
27 | numeric2 yellow ;
28 | string red ;
29 | comment gray i ;
30 | keyword purple ;
31 |
32 | // Keywords
33 | sample purple ;
34 | software yellow i ;
35 | commandline yellow ;
36 | chr green b ;
37 | chrStart green ;
38 |
39 | // Gradient
40 | gradbw1 teal ;
41 | gradbw3 teal b ;
42 | gradbw6 pink ;
43 | gradbw8 orange ;
44 | gradbw10 brightorange ;
45 | gradbw10b brightgreen b ;
46 | gradbw10i brightgreen i ;
--------------------------------------------------------------------------------
/syntax/less/faidx.lang:
--------------------------------------------------------------------------------
1 | # Fasta Index / Faidx (.fai) language definition file for less pipe
2 | # bioSyntax v0.1
3 | # Depends on sam.style + bioSyntax.outlang
4 |
5 | # faidx Data
6 | # Column 1: chr name
7 | environment push1 start '^(?=[\S])' begin
8 | drop = '$' exitall # stops multi-line searching
9 | chr = '^\S+'
10 |
11 | # Column 2: chr length
12 | environment push2 = '\t?' begin
13 | drop = '(?=$)' exitall
14 | chrStart = '\A\d+'
15 |
16 | # Column 3: genome total length (sum)
17 | environment push3 = '\t?' begin
18 | drop = '(?=$)' exitall
19 | numeric = '\A\d+'
20 |
21 | # Column 4: fasta column width
22 | # Column 5: fasta index #
23 | environment push4 = '\t?' begin
24 | drop = '(?=$)' exitall
25 | comment = '[\d\t]+'
26 |
27 | end # col4
28 | end # col3
29 | end # col2
30 | end # bed data section
31 |
--------------------------------------------------------------------------------
/docs/script/release:
--------------------------------------------------------------------------------
1 | #!/bin/sh
2 | # Tag and push a release.
3 |
4 | set -e
5 |
6 | # Make sure we're in the project root.
7 |
8 | cd $(dirname "$0")/..
9 |
10 | # Make sure the darn thing works
11 |
12 | bundle update
13 |
14 | # Build a new gem archive.
15 |
16 | rm -rf jekyll-theme-slate-*.gem
17 | gem build -q jekyll-theme-slate.gemspec
18 |
19 | # Make sure we're on the master branch.
20 |
21 | (git branch | grep -q 'master') || {
22 | echo "Only release from the master branch."
23 | exit 1
24 | }
25 |
26 | # Figure out what version we're releasing.
27 |
28 | tag=v`ls jekyll-theme-slate-*.gem | sed 's/^jekyll-theme-slate-\(.*\)\.gem$/\1/'`
29 |
30 | # Make sure we haven't released this version before.
31 |
32 | git fetch -t origin
33 |
34 | (git tag -l | grep -q "$tag") && {
35 | echo "Whoops, there's already a '${tag}' tag."
36 | exit 1
37 | }
38 |
39 | # Tag it and bag it.
40 |
41 | gem push jekyll-theme-slate-*.gem && git tag "$tag" &&
42 | git push origin master && git push origin "$tag"
43 |
--------------------------------------------------------------------------------
/docs/_site/script/release:
--------------------------------------------------------------------------------
1 | #!/bin/sh
2 | # Tag and push a release.
3 |
4 | set -e
5 |
6 | # Make sure we're in the project root.
7 |
8 | cd $(dirname "$0")/..
9 |
10 | # Make sure the darn thing works
11 |
12 | bundle update
13 |
14 | # Build a new gem archive.
15 |
16 | rm -rf jekyll-theme-slate-*.gem
17 | gem build -q jekyll-theme-slate.gemspec
18 |
19 | # Make sure we're on the master branch.
20 |
21 | (git branch | grep -q 'master') || {
22 | echo "Only release from the master branch."
23 | exit 1
24 | }
25 |
26 | # Figure out what version we're releasing.
27 |
28 | tag=v`ls jekyll-theme-slate-*.gem | sed 's/^jekyll-theme-slate-\(.*\)\.gem$/\1/'`
29 |
30 | # Make sure we haven't released this version before.
31 |
32 | git fetch -t origin
33 |
34 | (git tag -l | grep -q "$tag") && {
35 | echo "Whoops, there's already a '${tag}' tag."
36 | exit 1
37 | }
38 |
39 | # Tag it and bag it.
40 |
41 | gem push jekyll-theme-slate-*.gem && git tag "$tag" &&
42 | git push origin master && git push origin "$tag"
43 |
--------------------------------------------------------------------------------
/syntax/sublime/clustal.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Clustal syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: clustal
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [clustal]
9 | scope: text.clustal
10 |
11 | contexts:
12 | main:
13 | # Main Identifier
14 | - match: "^CLUSTAL.*"
15 | scope: comment
16 |
17 | # Sequence Identifier
18 | - match: "/[0-9]*-[0-9]*" #Optional sequence range
19 | scope: chrStart
20 |
21 | - match: "^[\\w\\.\\-\\_ ]*(?=[/ ])"
22 | scope: string
23 |
24 | # match Adenosine
25 | - match: "[Aa]++"
26 | scope: ntA
27 | # match Cytidine
28 | - match: "[Cc]++"
29 | scope: ntC
30 | # match Guanine
31 | - match: "[Gg]++"
32 | scope: ntG
33 | # match Thymidine/Uridine
34 | - match: "[TtUu]++"
35 | scope: ntT
36 | # aNy or unknown (X)
37 | - match: "[NnXx]++"
38 | scope: ntN
39 | # indel
40 | - match: "-"
41 | scope: ntGap
42 |
--------------------------------------------------------------------------------
/syntax/vim/fasta-hc.vim:
--------------------------------------------------------------------------------
1 | if exists("syntax_on")
2 | syntax reset
3 | colorscheme bioSyntax
4 | set nowrap
5 | endif
6 |
7 | " To be implemented:
8 | " Command to switch between types of fasta coloring
9 | " from vim terminal directly
10 | "
11 | " For now to use High Contrast theme,
12 | " rename this file in ~/.vim/syntax/:
13 | " "fasta-hc.vim" --> "fasta.vim"
14 |
15 |
16 | " In the future, implement 'context-aware' fasta
17 | " in which Nucleotides vs. Amino Acid sequences are detected
18 | " and colored accordingly
19 |
20 | syntax match headerbw ">.*$"
21 | syntax match hcA "[Aa]"
22 | syntax match hcG "[Gg]"
23 | syntax match hcC "[Cc]"
24 | syntax match hcT "[Tt]"
25 | syntax match hcU "[Uu]"
26 | syntax match hcR "[Rr]"
27 | syntax match hcY "[Yy]"
28 | syntax match hcS "[Ss]"
29 | syntax match hcW "[Ww]"
30 | syntax match hcM "[Mm]"
31 | syntax match hcK "[Kk]"
32 | syntax match hcD "[Dd]"
33 | syntax match hcB "[Bb]"
34 | syntax match hcV "[Vv]"
35 | syntax match hcH "[Hh]"
36 | syntax match hcN "[Nn]"
37 | syntax match hcGap "[/\-/\.]"
38 |
--------------------------------------------------------------------------------
/syntax/less/fastq.lang:
--------------------------------------------------------------------------------
1 | # Fasta language definition file for less pipe
2 | # bioSyntax v0.1
3 | # Depends on fasta.style + bioSyntax.outlang
4 |
5 | # Row 1: Header
6 | # Entry header start with @
7 | environment header = '^.+' begin # Header line
8 |
9 | # Row 2: nt Seq
10 | environment ntSeq = '^(?=[ATCG])' begin
11 | ntA = '[Aa]++'
12 | ntT = '[Tt]++'
13 | ntG = '[Gg]++'
14 | ntC = '[Cc]++'
15 | ntT = '[Uu]++'
16 | ntN = '[NnXx]++'
17 |
18 | # Row 3: Comment Line
19 | environment comment = '^\+' begin # Comment line
20 |
21 | #Row 4: PHRED score
22 | environment phred = '^' begin
23 | drop = '$' exitall
24 | # Illumina 1.8 Scale
25 | # !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJ...j
26 | # | | | | | | | | | |...
27 | gradbw1 = '\A[!-%]++'
28 | gradbw3 = '\A[!-(]++'
29 | gradbw6 = '\A[)-0]++'
30 | gradbw8 = '\A[1-8]++'
31 | gradbw10 = '\A[9-@]++'
32 | gradbw10b = '\A[A-D]++'
33 | gradbw10i = '\A[E-j]++'
34 | end
35 | end
36 | end
37 | end
--------------------------------------------------------------------------------
/examples/nt-seq/test_gcContent.fa:
--------------------------------------------------------------------------------
1 | >cMyc_exon2_0.646gc
2 | GGCGGTGTCTCCTCATGGAGCACCAGGGGCTCGGGGCTGCCCTGCGGGGA
3 | GGACTCCGTCGAGGAGAGCAGAGAATCCGAGGACGGAGAGAAGGCGCTGG
4 | AGTCTTGCGAGGCGCAGGACTTGGGCGAGCTGCTGTCGTTGAGAGGGTAG
5 | GGGAAGACCACCGAGGGGTCGATGCACTCTGAGGCGGCGGCGCTCAGATC
6 | CTGCAGGTACAAGCTGGAGGTGGAGCAGACGCTGTGGCCGCGGGCGGGGT
7 | TCGGGCTGCCGCTGTCTTTGCGCGCAGCCTGGTAGGAGGCCAGCTTCTCT
8 | GAGACGAGCTTGGCGGCGGCCGAGAAGCCGCTCCACATACAGTCCTGGAT
9 | GATGATGTTTTTGATGAAGGTCTCGTCGTCCGGGTCGCAGATGAAACTCT
10 | GGTTCACCATGTCTCCTCCCAGCAGCTCGGTCACCATCTCCAGCTGGTCG
11 | GCCGTGGAGAAGCTCCCGCCACCGCCGTCGTTGTCTCCCCGAAGGGAGAA
12 | >cMyc_3'UTR_0.278gc
13 | ACAAAACATTCACAACTTAAGATTTGGCTCAATGATATATTTGCCAGTTA
14 | TTTTATTTTTTCTAAAAACAATAGAAAAAAATCAACTTTAAAAAGCAAAA
15 | TGTACTTAAATAAAAAAAATTAGGGTTTATAGTACCTATAATACTAGGTA
16 | CTATATACTAGGATTGAAATTCTGTGTAACTGCTATAAACGTTTTATTAA
17 | AGTTATTTACATTTAATGGCAATATTTACAGAGAAACATTGTGTAAATCT
18 | TAAAATTTTTTAAAAACAATTCTTAAATACAAATCTGTTAAAGAAAAAAA
19 | AAAGATGGTAAGCATAAAAAAGTTCTTTTATGCCCAAAGTCCAATTTGAG
20 | GCAGTTTACATTATGGCTAAATCTTTCAGTCTCAAGACTCAGCCAAGGTT
21 | GTGAGGTTGCATTTGATCATGCATTTGAAACAAGTTCATAGGTGATTGCT
22 | CAGGACATTTCTGTTAGAAGGAATCGTTTTCCTTACTTTTCCTTACGCAC
23 |
--------------------------------------------------------------------------------
/syntax/vim/faidx.vim:
--------------------------------------------------------------------------------
1 | " Vim syntax file
2 | " Language: faidx
3 | " Filetypes: .fai, .faidx
4 | " Maintainer: bioSyntax
5 | " Version: v0
6 |
7 | if exists("syntax_on")
8 | syntax reset
9 | colorscheme bioSyntax
10 | endif
11 |
12 | " Robust Column Selection in Vim Syntax
13 | " -- This logic can be extended for N columns
14 | " -- To add highlighting to a column add it to the contains list (submatch)
15 | syntax region chr matchgroup=chr start='^' end='\n' contains=chrStart
16 | syntax region chrStart matchgroup=chrStart start='\t' end='\n\@=' contains=numeric2,submatch
17 | syntax region numeric2 matchgroup=numeric2 start='\t' end='\n\@=' contains=Col4
18 | syntax region Col4 matchgroup=Col4 start='\t' end='\n\@=' contains=Col5
19 | syntax region Col5 matchgroup=Col5 start='\t' end='\n\@=' contains=Col6
20 | syntax region Col6 matchgroup=Col6 start='\t' end='\n\@='
21 |
22 | " Submatch Definitions
23 | syntax match submatch '3' contained
24 |
25 |
26 | " Highlighting / Theme Control
27 | " =========================================================
28 | highlight link Col4 numeric
29 | highlight link Col5 numeric
30 | highlight link Col6 numeric
31 |
32 | highlight submatch ctermfg=28
33 |
--------------------------------------------------------------------------------
/syntax/sublime/faidx.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Fasta Index (faidx) syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: faidx
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [fai,fai]
9 | scope: source.faidx
10 |
11 | # Fasta Index Filetype Description
12 | # NAME Name of this reference sequence
13 | # LENGTH Total length of this reference sequence, in bases
14 | # OFFSET Offset within the FASTA file of this sequence's first base
15 | # LINEBASES The number of bases on each line
16 | # LINEWIDTH The number of bytes in each line, including the newline
17 |
18 | contexts:
19 | main:
20 | # COLUMN 1
21 | - match: '^[\S]*\t'
22 | scope: chr.faidx
23 | push: contig.length
24 |
25 | # COLUMN 3
26 | - match: '(?<=\t)[\S]*\t'
27 | scope: numeric.faidx
28 | push: genomic.offset
29 |
30 | # COLUMN 5
31 | - match: '[\S]*$'
32 | scope: comment.faidx
33 |
34 | contig.length:
35 | # COLUMN 2
36 | - match: '[\S]*'
37 | scope: chrStart.faidx
38 | - match: \t
39 | pop: true
40 |
41 | genomic.offset:
42 | # COLUMN 4
43 | - match: '[\S]*'
44 | scope: comment.faidx
45 | - match: \t
46 | pop: true
--------------------------------------------------------------------------------
/examples/nt-seq/test_gcContent_randomer_gradient.fa:
--------------------------------------------------------------------------------
1 | >randomer_gc_gradient_0.0-1.0
2 | TTAATTAAATTTATTAAATTTTTATATTTAAAATTTTAATATTATATTAT
3 | TAAAAATTAATTATTATTATTAAAATTTTATTTAAAAATATTTTAATTTA
4 | TATTTTTATTACGTTTTTAAATAACTAGTAATAAATATCTTTCATAAATG
5 | AAAATTTTTTTTATTAATAATTATATTAAAATGTTTTTAAATTTTTTCAT
6 | TTAAATGAAAATAAACACAGAATAATAATTACTTTTTTGATACGTGAAAC
7 | ATATTCCATAGTAATTTAAAGATTTGAAAATTTATCACTTCTAGGATTCT
8 | TGTGAGATGTTATAGAACTTCTGGTTCATCTCGTAGGATATCAAGCTTTA
9 | TTTTAATAAAGCTTTCCATTCGAGTATAGCAGAAAAAACGCTTACTGAAT
10 | AATGAAAAACCTATGGACTTTGTTTAGGGTAGCATCAGAAATCTAAACCT
11 | TCAGAAAGTGAAGATCCCGAGTATAGACCTTTATCTGCGGTTCAAGTTAA
12 | AGGGCACCCTGTAGTTGGAAGGGGAACTATTTCGTGGGGCGAGCCCATAC
13 | CGTCTCTCTTGCGGAAGACTTAACACGATAGGAAGCTGGAATAGTTTCGA
14 | CATCGTGGCCCTTAGACTTCGCACACTTACACCCGCACCGCGCGCATGTG
15 | GAATTAGAGGCGAGGTACGATCCCTAGACCGACGTACGATGCAACTGTGT
16 | TAGAGCGCCCCGCTCGGGCGTGGCAGTGAGCACGCCTTCTCAGTTGTGCC
17 | AACCCTCGTCCTCACCGAAGCTTGGAGCCAATGATCAGGATCGCTGCCTC
18 | CCCCGGCGTGGCGCGCGTGCGGCTCAACCACCGCTCCATGCCAGGGCGCC
19 | GGCTGCATGCCGGGTTGACACGCCCGCGCCGCCCGGGGAGAATATGCGAG
20 | CCGTGCGGCGGGGGCAAGGCCGCTGGGGGCGGGGGCGGCCCCGGACCCCG
21 | CCTACCGCTGCCGGCGAGGGGCCCCCGTCTGGGGGGCGGGTGTCGGCCGG
22 | CCGGGGGGCCGCGCCCCCGCGGCCGGCGCGCGGCCCGGCCCCGCCGGCGC
23 | GGCGGCGCCCCCGCCGGCGCCCCGCCCGCCGGGCCCCCCCCGCGGCGGGG
24 |
--------------------------------------------------------------------------------
/syntax/less/vcf.style:
--------------------------------------------------------------------------------
1 | // VCF Style File -- less
2 | // bioSyntax v0.1
3 |
4 | // Header ID
5 | header black b ;
6 |
7 | // Nucleotide Coloring
8 | ntA darkgreen ;
9 | ntC darkred ;
10 | ntG brown ;
11 | ntT darkblue ;
12 | ntN teal i ;
13 |
14 | // Switch (Good / Bad)
15 | bon darkblue ;
16 | nob darkblue u ;
17 | mal darkred ;
18 | lam darkred u ;
19 |
20 | // Class
21 | version blue b ;
22 | comment gray i ;
23 |
24 | numeric blue ;
25 | numeric2 yellow ;
26 |
27 | string red ;
28 | quoteString red i ;
29 |
30 | url purple ;
31 |
32 | // Was keyword6
33 | keyword red ;
34 | keywordb red b ;
35 | keywordi red i ;
36 | keydrow red u ;
37 |
38 | // keyword2
39 | keyword2 brightgreen ;
40 | keywordb2 brightgreen b ;
41 | keywordi2 brightgreen i;
42 | keydrow2 brightgreen u ;
43 |
44 | // Was keyword
45 | keyword3 purple ;
46 | keywordb3 purple b ;
47 | keywordi3 purple i ;
48 | keydrow3 purple u ;
49 |
50 | keyword4 orange ;
51 | keywordi4 orange i ;
52 | keydrow4 orange u ;
53 |
54 | // Was Keyword2
55 | keyword5 cyan ;
56 | keywordi5 cyan i ;
57 | keydrow5 cyan u ;
58 |
59 | keyword6 pink ;
60 | keywordi6 pink i ;
61 | keydrow6 pink u ;
62 |
63 | // Biological Classes
64 | sample purple ;
65 |
66 | software yellow i ;
67 | commandline yellow ;
68 |
69 | chr green b ;
70 | chrStart green ;
71 |
72 | grad4 brightgreen b ;
73 | grad5 brightgreen i ;
74 |
--------------------------------------------------------------------------------
/examples/nt-seq/test3.fasta:
--------------------------------------------------------------------------------
1 | >PHOKE_DN21123
2 | VP*FPACNPRRHIIRSSIFS*FF*KNIFFNPKRRIIAINFFLFI*DVQTFSNLEDSPQTL
3 | THVRKKIKSSLRI*CSVLKLTDVE*KRPFRQLNYKFFQA*CTLFF*YVFKINLIIPVILP
4 | EPIYNDILTIFGIGFQLSVQR*CFRRKPSRFKLSQSTV*FVLQFYMFVTLSSKVQKMS*Q
5 | LSTHS**ATYPYFQPMAQLRGGFRVILSRTRKIGT
6 | >PHOKE_DN21456
7 | VFISFKNIRTLALQQVINKFYLY**KIRFLKNKGL*NEIV**IHTCKRYESKQYIYFLF*
8 | NAILIYNE*MRLAPL*NSTVY*QSTDLPTEIKLSLR*NLSYISTIC*VICQNQSS*ITDG
9 | NKFRNQIHKS*FQLFFFQDHMMEITGDKINEGQSYADGPCGDRKHYQILNARGSEYVENT
10 | GHNFQIHNR*SILINDFIFKKSNLYSLSEIIFLICMRNIK*YLQIVIFKVLNVSYKHRKV
11 | KKHKETFK*FKDGYIISTYHFKLAFHINFTCTDLHI*EFVNIFYQSQSGQSAELSP*HTP
12 | EV*LSHDI*YIKK*LSNCNIPTL*EEEEGGGGGTTTTAAA
13 |
14 | >seq1_head
15 | GCTGACACGCTGTCCTCTGGCGACCTGTCGTCGGAGAGGTTGGGCCTCCG
16 | GATGCGCGCGGGGCTCTGGCCTCACGGTGACCGGCTAGCCGGCCGCGCTC
17 | CTGCCTTGAGCCGCCTGCCGCGGCCCGCGGGCCTGCTGTTCTCTCGCGCG
18 | TCCGAGCGTCCCGACTCCCGGTGCCGGCCCGGGTCCGGGTCTCTGACCCA
19 | CCCGGGGGCGGCGGGGAAGGCGGCGAGGGCCACCGTGCCCCGTGCGCTCT
20 | CCGCTGCGGGCGCCCGGGGCGCCGCACAACCCCACCCGCTGGCTCCGTGC
21 | CGTGCGTGTCAGGCGTTCTCGTCTCCGCGGGGTTGTCCGCCGCCCCTTCC
22 | CCGGAGTGGGGGGTGGCCGGAGCCGATCGGCTCGCTGGCCGGCCGGCCTC
23 | CGCTCCCGGGGGGCTCTTCGATCGATGTGGTGACGTCGTGCTCTCCCGGG
24 | >seq2_tail:1234
25 | ggggttttaaaaacccccD-------------------------------
26 | GTTTGGGAGCCGCGGAGGCGCCGCGCCGAGCCGGGCCCCGTGGCCCGCCG
27 | CCCGGGGGCGGCGGGGAAGGCGGCGAGGGCCACCGTGCCCCGTGCGCTCT
28 | CACCCGGCCGACCTCCGCTCGCGACCTCTCCTCGGTCGGGCCTCCGGGGTD
29 | CGACCGCCTGNNNnnnGCGTGAGACT...TG--GGCGTCTCGCCGTGTCC
30 |
--------------------------------------------------------------------------------
/syntax/sublime/fasta.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Fasta-Nucleotides syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: fasta
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [.fasta,.fa,.fas,.mfa]
9 | scope: text.fasta
10 |
11 |
12 | contexts:
13 | main:
14 | # Fasta Header
15 | - match: "^>.*"
16 | scope: header
17 |
18 | # Match Nucleotides
19 | # match Adenosine
20 | - match: "[Aa]++"
21 | scope: ntA
22 |
23 | # match Cytidine
24 | - match: "[Cc]++"
25 | scope: ntC
26 |
27 | # match Guanine
28 | - match: "[Gg]++"
29 | scope: ntG
30 |
31 | # match Thymidine
32 | - match: "[Tt]++"
33 | scope: ntT
34 |
35 | # match Uridine
36 | - match: "[Uu]++"
37 | scope: ntU
38 |
39 | # match aNy or unknown (X)
40 | - match: "[NnXx]++"
41 | scope: ntN
42 |
43 | # indel
44 | - match: "[-]"
45 | scope: ntGap
46 |
47 | # Match Extended Nucleotides
48 | - match: "[Rr]++"
49 | scope: ntR
50 | - match: "[Yy]++"
51 | scope: ntY
52 | - match: "[Ss]++"
53 | scope: ntS
54 | - match: "[Ww]++"
55 | scope: ntW
56 | - match: "[Mm]++"
57 | scope: ntM
58 | - match: "[Kk]++"
59 | scope: ntK
60 | - match: "[Dd]++"
61 | scope: ntD
62 | - match: "[Bb]++"
63 | scope: ntB
64 | - match: "[Vv]++"
65 | scope: ntV
66 | - match: "[Hh]++"
67 | scope: ntH
68 |
69 |
--------------------------------------------------------------------------------
/syntax/sublime/fasta-hc.sublime-syntax:
--------------------------------------------------------------------------------
1 | %YAML 1.2
2 | ---
3 | # Fasta-Nucleotides syntax highlighting file
4 | # Maintainer: bioSyntax.org
5 | # Version: v0.1
6 | name: fasta
7 | # See http://www.sublimetext.com/docs/3/syntax.html
8 | file_extensions: [.fasta,.fa,.fas,.mfa]
9 | scope: text.fasta
10 |
11 |
12 | contexts:
13 | main:
14 | # Fasta Header
15 | - match: "^>.*"
16 | scope: header
17 |
18 | # Match Nucleotides
19 | # match Adenosine
20 | - match: "[Aa]++"
21 | scope: ntA
22 |
23 | # match Cytidine
24 | - match: "[Cc]++"
25 | scope: ntC
26 |
27 | # match Guanine
28 | - match: "[Gg]++"
29 | scope: ntG
30 |
31 | # match Thymidine
32 | - match: "[Tt]++"
33 | scope: ntT
34 |
35 | # match Uridine
36 | - match: "[Uu]++"
37 | scope: ntU
38 |
39 | # match aNy or unknown (X)
40 | - match: "[NnXx]++"
41 | scope: ntN
42 |
43 | # indel
44 | - match: "[-]"
45 | scope: ntGap
46 |
47 | # Match Extended Nucleotides
48 | - match: "[Rr]++"
49 | scope: ntR
50 | - match: "[Yy]++"
51 | scope: ntY
52 | - match: "[Ss]++"
53 | scope: ntS
54 | - match: "[Ww]++"
55 | scope: ntW
56 | - match: "[Mm]++"
57 | scope: ntM
58 | - match: "[Kk]++"
59 | scope: ntK
60 | - match: "[Dd]++"
61 | scope: ntD
62 | - match: "[Bb]++"
63 | scope: ntB
64 | - match: "[Vv]++"
65 | scope: ntV
66 | - match: "[Hh]++"
67 | scope: ntH
68 |
69 |
--------------------------------------------------------------------------------
/syntax/vim/fastq.vim:
--------------------------------------------------------------------------------
1 | if exists("syntax_on")
2 | syntax reset
3 | colorscheme bioSyntax
4 | set nowrap
5 | endif
6 |
7 | syntax match gradbw1 "[/\!-/\$]" contained
8 | syntax match gradbw2 "[/\%-/\(]" contained
9 | syntax match gradbw3 "[/\)-/\,]" contained
10 | syntax match gradbw4 "[/\--/\/]" contained
11 | syntax match gradbw5 "[0-4]" contained
12 | syntax match gradbw6 "[5-9]" contained
13 | syntax match gradbw7 "[/\:/\;/\<]" contained
14 | syntax match gradbw8 "[/\=/\>/\?/\@]" contained
15 | syntax match gradbw9 "[A-E]" contained
16 | syntax match gradbw10 "[F-J]" contained
17 |
18 | syntax region headerbw start="^@\{1,2}.*$" end="\n\@="
19 | syntax region bases start="^[ACGT]\{10,}" end=".*$" contains=ntA,ntG,ntC,ntT
20 | syntax region comment2 start="\([ACGT]\{10,}\)\@<=" end="\n\@="
21 | syntax region quality start="\(+*$\n\@=\)\@<=.*" end="\n\@=" contains=gradbw1,gradbw2,gradbw3,gradbw4,gradbw5,gradbw6,gradbw7,gradbw8,gradbw9,gradbw10
22 |
23 | syntax match ntA "A" contained
24 | syntax match ntG "G" contained
25 | syntax match ntC "C" contained
26 | syntax match ntT "T" contained
27 |
28 | "highlight header ctermfg=100
29 | "highlight com ctermfg=20
30 | "highlight qual0 ctermfg=DarkGrey
31 | "highlight qual1 ctermfg=Grey
32 | "highlight qual2 ctermfg=Red
33 | "highlight qual3 ctermfg=DarkRed
34 |
35 | "highlight ntA ctermfg=Black ctermbg=Green guibg=#272822
36 | "highlight ntG ctermfg=Black ctermbg=Yellow guibg=#FF8C00
37 | "highlight ntC ctermfg=Black ctermbg=Blue guibg=#2A0AFD
38 | "highlight ntT ctermfg=Black ctermbg=Red guibg=#FD0A0A
39 |
--------------------------------------------------------------------------------
/syntax/vim/clustal.vim:
--------------------------------------------------------------------------------
1 | " Vim syntax file
2 | " Language: clustal
3 | " Filetypes: .clustal
4 | " Maintainer: bioSyntax
5 | " Version: v0
6 |
7 | if exists("syntax_on")
8 | syntax reset
9 | colorscheme bioSyntax
10 | endif
11 |
12 | " REGEX Engine
13 | " =========================================================
14 |
15 | " Nucleotide matching
16 | syntax match ntA "[Aa]"
17 | syntax match ntG "[Gg]"
18 | syntax match ntC "[Cc]"
19 | syntax match ntT "[Tt]"
20 | syntax match ntU "[Uu]"
21 | syntax match ntR "[Rr]"
22 | syntax match ntY "[Yy]"
23 | syntax match ntS "[Ss]"
24 | syntax match ntW "[Ww]"
25 | syntax match ntM "[Mm]"
26 | syntax match ntK "[Kk]"
27 | syntax match ntD "[Dd]"
28 | syntax match ntB "[Bb]"
29 | syntax match ntV "[Vv]"
30 | syntax match ntH "[Hh]"
31 | syntax match ntN "[Nn]"
32 | syntax match ntGap "[/\-/\.]"
33 |
34 | " Sequence Name
35 | syntax match comment '\S*\s'
36 |
37 | " Header starts with CLUSTAL
38 | syntax match header "CLUSTAL.*"
39 |
40 |
41 | " Highlighting / Theme Control
42 | " =========================================================
43 |
44 | "highlight header ctermfg=Black ctermbg=8
45 | "highlight comment ctermfg=8
46 |
47 | "highlight ntA ctermfg=Black ctermbg=10 guibg=#47ff19
48 | "highlight ntG ctermfg=Black ctermbg=214 guibg=#f09000
49 | "highlight ntC ctermfg=Black ctermbg=9 guibg=#ff4641
50 | "highlight ntT ctermfg=Black ctermbg=33 guibg=#4192ff
51 | highlight ntU ctermfg=Black ctermbg=13 guibg=#8a89ff
52 | "highlight ntN ctermfg=8 ctermbg=15 guibg=#ffffff
53 | " highlight ntGap #No Highlight
54 |
--------------------------------------------------------------------------------
/syntax/less/pdb.style:
--------------------------------------------------------------------------------
1 | // PDB Style File -- less
2 | // bioSyntax v0.1
3 |
4 | // Header ID
5 | header black b ;
6 |
7 | // Nucleotide Coloring
8 | ntA darkgreen ;
9 | ntC darkred ;
10 | ntG brown ;
11 | ntT darkblue ;
12 | ntN teal i ;
13 |
14 | // Amino Acid Coloring (CLUSTALX)
15 | aaHydro brightorange ; // A I L M F W V
16 | aaPos red ; // K R
17 | aaNeg cyan ; // E D
18 | aaPol green ; // N Q S T
19 | aaCys red ; // C (supposed to be pink)
20 | aaGly orange ; // G
21 | aaPro pink ; // P
22 | aaAro purple ; // H Y
23 |
24 | // Switch (Good / Bad)
25 | bon darkblue ;
26 | nob darkblue u ;
27 | mal darkred ;
28 | lam darkred u ;
29 |
30 | // Class
31 | version blue b ;
32 | comment gray i ;
33 |
34 | numeric blue ;
35 | numeric2 yellow ;
36 |
37 | string red ;
38 | quoteString red i ;
39 |
40 | url purple ;
41 |
42 | // Was keyword6
43 | keyword red ;
44 | keywordb red b ;
45 | keywordi red i ;
46 | keydrow red u ;
47 |
48 | // keyword2
49 | keyword2 brightgreen ;
50 | keywordb2 brightgreen b ;
51 | keywordi2 brightgreen i;
52 | keydrow2 brightgreen u ;
53 |
54 | // Was keyword
55 | keyword3 purple ;
56 | keywordb3 purple b ;
57 | keywordi3 purple i ;
58 | keydrow3 purple u ;
59 |
60 | keyword4 orange ;
61 | keywordi4 orange i ;
62 | keydrow4 orange u ;
63 |
64 | // Was Keyword2
65 | keyword5 cyan ;
66 | keywordi5 cyan i ;
67 | keydrow5 cyan u ;
68 |
69 | keyword6 pink ;
70 | keywordi6 pink i ;
71 | keydrow6 pink u ;
72 |
73 | // Biological Classes
74 | sample purple ;
75 |
76 | software yellow i ;
77 | commandline yellow ;
78 |
79 | chr green b ;
80 | chrStart green ;
81 |
82 | grad4 brightgreen b ;
83 | grad5 brightgreen i ;
84 |
--------------------------------------------------------------------------------
/syntax/gedit/faidx.lang:
--------------------------------------------------------------------------------
1 |
2 |
12 |