├── Install_bioSyntax.sh ├── LICENSE.md ├── README.md ├── bioSyntax_talk.pptm ├── docs ├── .sass-cache │ └── 68710e094d770af080a52dddf9b6dabfc7ddb404 │ │ ├── jekyll-theme-slate.scssc │ │ └── rouge-github.scssc ├── CNAME ├── Gemfile ├── Gemfile.lock ├── _config.yml ├── _layouts │ └── default.html ├── _sass │ ├── jekyll-theme-slate.scss │ └── rouge-github.scss ├── _site │ ├── CNAME │ ├── Gemfile │ ├── Gemfile.lock │ ├── assets │ │ ├── css │ │ │ └── style.css │ │ └── images │ │ │ ├── FastaBanner.png │ │ │ ├── bg_hr.png │ │ │ ├── bioSyntax_logo.png │ │ │ ├── blacktocat.png │ │ │ ├── blacktocat2.png │ │ │ ├── hackseq_logo_sq_inv_Solid.png │ │ │ ├── hackseq_logo_sq_inv_icon.png │ │ │ ├── icon_download.png │ │ │ ├── sam-less.png │ │ │ ├── sam-less_command.png │ │ │ └── sprite_download.png │ ├── index.md │ └── script │ │ ├── bootstrap │ │ ├── cibuild │ │ └── release ├── assets │ ├── css │ │ └── style.scss │ └── images │ │ ├── FastaBanner.png │ │ ├── bg_hr.png │ │ ├── bioSyntax_logo.png │ │ ├── blacktocat.png │ │ ├── blacktocat2.png │ │ ├── hackseq_logo_sq_inv_Solid.png │ │ ├── hackseq_logo_sq_inv_icon.png │ │ ├── icon_download.png │ │ ├── sam-less-small.gif │ │ ├── sam-less.png │ │ ├── sam-less_2.png │ │ ├── sam-less_command.gif │ │ ├── sam-less_command.png │ │ └── sprite_download.png ├── collaborate.md ├── formats.md ├── index.md ├── install.md ├── manual.md └── script │ ├── bootstrap │ ├── cibuild │ └── release ├── examples ├── annot │ ├── test.bedpe │ ├── test1.bed │ ├── test1.wig │ ├── test2.wig │ ├── test_cufflinks.gtf │ ├── test_gencode.gtf │ └── test_refseqUCSC.gtf ├── nt-seq │ ├── bioSyntax.fa │ ├── test1.fa │ ├── test1.fq │ ├── test1_prot.faa │ ├── test2.fa │ ├── test2.fq │ ├── test2.fq.gz │ ├── test3.fasta │ ├── test_alignment1.clustal │ ├── test_alignment1.mfa │ ├── test_alignment1.phylip │ ├── test_alignment2.clustal │ ├── test_gcContent.fa │ ├── test_gcContent_randomer.fa │ └── test_gcContent_randomer_gradient.fa ├── pdb │ ├── pdbx.link │ ├── test.pdb │ ├── test2.pdb │ └── test2.pdbx ├── sam │ ├── mario.sam │ ├── test.fa.fai │ ├── test.flagstat │ ├── test1.sam │ ├── test2.sam │ └── test4_large.sam └── vcf │ ├── test.vcf │ ├── test_1000genomes.vcf.gz │ └── test_dbSNP.vcf ├── syntax ├── archive │ └── bioSyntax_sublime_v171022.zip ├── bioSyntax_sublime_RELEASE.zip ├── gedit │ ├── bed.lang │ ├── bioKate.xml │ ├── bioSyntax.lang │ ├── bioSyntax.xml │ ├── clustal.lang │ ├── faidx.lang │ ├── fasta-clustal.lang │ ├── fasta-hc.lang │ ├── fasta-hydrophobicity.lang │ ├── fasta-taylor.lang │ ├── fasta-zappo.lang │ ├── fasta.lang │ ├── fastq.lang │ ├── gtf.lang │ ├── quickInstall_unix.sh │ ├── sam.lang │ ├── vcf.lang │ └── wig.lang ├── less │ ├── bed.lang │ ├── bioSyntax-vcf.outlang │ ├── bioSyntax.outlang │ ├── bp_append.txt │ ├── clustal.lang │ ├── faidx.lang │ ├── fasta.lang │ ├── fasta.style │ ├── fastq.lang │ ├── flagstat.lang │ ├── gtf.lang │ ├── pdb.lang │ ├── pdb.style │ ├── quickInstall.sh │ ├── rc_append.txt │ ├── sam.lang │ ├── sam.style │ ├── src-hilite-lesspipe_BIO.sh │ ├── vcf.lang │ └── vcf.style ├── sublime │ ├── Color Scheme - bioSyntax.sublime-package │ ├── bed.sublime-syntax │ ├── clustal.sublime-syntax │ ├── faidx.sublime-syntax │ ├── fasta-clustal.sublime-syntax │ ├── fasta-hc.sublime-syntax │ ├── fasta-hydro.sublime-syntax │ ├── fasta-taylor.sublime-syntax │ ├── fasta-zappo.sublime-syntax │ ├── fasta.sublime-syntax │ ├── fastq.sublime-syntax │ ├── flagstat.sublime-syntax │ ├── gtf.sublime-syntax │ ├── pdb.sublime-syntax │ ├── sam.sublime-syntax │ ├── vcf.sublime-syntax │ └── wig.sublime-syntax └── vim │ ├── bed.vim │ ├── clustal.vim │ ├── colors │ └── bioSyntax.vim │ ├── faidx.vim │ ├── fasta-hc.vim │ ├── fasta.vim │ ├── fastq.vim │ ├── ftdetect │ ├── bed.vim │ ├── clustal.vim │ ├── faidx.vim │ ├── fasta.vim │ ├── fastq.vim │ ├── gtf.vim │ ├── pdb.vim │ ├── sam.vim │ └── vcf.vim │ ├── gtf.vim │ ├── pdb.vim │ ├── quickInstall_unix.sh │ ├── sam.vim │ └── vcf.vim └── theme ├── gedit ├── bioKate.xml └── bioSyntax.xml └── sublime ├── Color Scheme - Default_BACKUP.sublime-package ├── Color Scheme - bioSyntax.sublime-package └── Color Scheme - bioSyntax_PRE-UNIFICATION.sublime-package /README.md: -------------------------------------------------------------------------------- 1 | ![bioSyntax Logo](dev/img/bioSyntax_logo.png) 2 | 3 | # ARCHIVED REPOSITORY 4 | # SEE: [bioSyntax Repository](https://github.com/bioSyntax/bioSyntax) FOR NEW VERSIONS 5 | -------------------------------------------------------------------------------- /bioSyntax_talk.pptm: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ababaian/bioSyntax-archive/4a86b38c2f348694786a066f275a0ede79d471af/bioSyntax_talk.pptm -------------------------------------------------------------------------------- /docs/.sass-cache/68710e094d770af080a52dddf9b6dabfc7ddb404/jekyll-theme-slate.scssc: 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jekyll-theme-slate 2 | title: bioSyntax 3 | description: Human Readable Biology 4 | url: http://bioSyntax.org 5 | 6 | markdown: kramdown 7 | gems: 8 | - jekyll-redirect-from 9 | -------------------------------------------------------------------------------- /docs/_layouts/default.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | {% seo %} 13 | 14 | 15 | 16 | 17 | 18 |
19 |
20 | View Source 21 | 22 |

bioSyntax:

23 | 24 | 25 | 26 | {% if site.show_downloads %} 27 |
28 | Download this project as a .zip file 29 | Download this project as a tar.gz file 30 |
31 | {% endif %} 32 |
33 |
34 | 35 | 36 |
37 |
38 | {{ content }} 39 |
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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/assets/images/FastaBanner.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ababaian/bioSyntax-archive/4a86b38c2f348694786a066f275a0ede79d471af/docs/_site/assets/images/FastaBanner.png -------------------------------------------------------------------------------- /docs/_site/assets/images/bg_hr.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ababaian/bioSyntax-archive/4a86b38c2f348694786a066f275a0ede79d471af/docs/_site/assets/images/bg_hr.png 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-------------------------------------------------------------------------------- /docs/_site/assets/images/sprite_download.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ababaian/bioSyntax-archive/4a86b38c2f348694786a066f275a0ede79d471af/docs/_site/assets/images/sprite_download.png -------------------------------------------------------------------------------- /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 | ![Example less command](assets/images/sam-less_command.png) 10 | ![Example .sam in less](assets/images/sam-less.png) 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 | -------------------------------------------------------------------------------- /docs/_site/script/bootstrap: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | set -e 4 | 5 | gem install bundler 6 | bundle install 7 | -------------------------------------------------------------------------------- /docs/_site/script/cibuild: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | set -e 4 | 5 | bundle exec jekyll build 6 | gem build jekyll-theme-slate.gemspec 7 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /docs/assets/css/style.scss: -------------------------------------------------------------------------------- 1 | --- 2 | --- 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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... -------------------------------------------------------------------------------- /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 | - -------------------------------------------------------------------------------- /docs/index.md: -------------------------------------------------------------------------------- 1 | [INSTALL](install.md) \| [USING BIOSYTNAX](manual.md) \| [FILE FORMATS](formats.md) \| [COLLABORATE](collaborate.md) 2 | 3 | Syntax highlighting for computational biology in `vim`, `less`, `sublime3` & `gedit`. 4 | 5 | ### [Watch our hackseq17 presentation (~5 min)](https://youtu.be/dHYN3E7edhY?t=6m28s) 6 | 7 | ![Example less command](assets/images/sam-less_command.gif) 8 | [](assets/images/sam-less.png) -------------------------------------------------------------------------------- /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. -------------------------------------------------------------------------------- /docs/manual.md: -------------------------------------------------------------------------------- 1 | # bioSyntax Manual 2 | 3 | To really appreciate your data, read this short manual on what all the bioSyntax colors mean. 4 | 5 | - Nucleotides 6 | - Amino Acids 7 | - PHRED Scores 8 | - Alignment + CIGAR strings 9 | - GTF/WIG score scaling 10 | - ... -------------------------------------------------------------------------------- /docs/script/bootstrap: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | set -e 4 | 5 | gem install bundler 6 | bundle install 7 | -------------------------------------------------------------------------------- /docs/script/cibuild: -------------------------------------------------------------------------------- 1 | #!/bin/sh 2 | 3 | set -e 4 | 5 | bundle exec jekyll build 6 | gem build jekyll-theme-slate.gemspec 7 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /examples/annot/test1.bed: -------------------------------------------------------------------------------- 1 | chr5 149433731 149433769 (CTG)n 225 + 2 | chr5 149434120 149434212 MIR 346 - 3 | chr5 149434267 149434583 AluJr 1964 + 4 | chr5 149436242 149436426 MIR 485 - 5 | chr5 149437240 149437536 L3 577 - 6 | chr5 149437537 149437696 MER5B 422 + 7 | chr5 149437704 149437857 MER5A1 419 - 8 | chr5 149438414 149438530 MIR3 304 + 9 | chr5 149438615 149438906 AluSp 2318 - 10 | chr5 149439015 149439073 L2c 232 + 11 | chr5 149439490 149439600 MIR3 215 + 12 | chr5 149439608 149439920 AluSc8 2455 + 13 | chr5 149441588 149441715 MIR3 288 + 14 | chr5 149441749 149441810 (TCCA)n 294 + 15 | chr5 149441824 149442183 L1MB2 1886 - 16 | chr5 149442193 149442379 L2a 525 - 17 | chr5 149442588 149442869 AluJb 1555 - 18 | chr5 149442918 149443073 AluJo 963 - 19 | chr5 149443548 149443863 L1PA16 1896 + 20 | chr5 149443886 149443942 L3 197 + 21 | chr5 149445529 149445681 L3 444 + 22 | chr5 149445794 149446002 MIRb 424 - 23 | chr5 149446010 149446147 MIR3 393 - 24 | chr5 149446678 149446891 MIRb 394 + 25 | chr5 149446888 149447084 MIRb 557 + 26 | chr5 149447213 149447258 L2c 183 + 27 | chr5 149447419 149447534 FLAM_A 702 - 28 | chr5 149447550 149447674 L2a 248 + 29 | chr5 149447796 149447821 (CAG)n 192 + 30 | chr5 149447955 149448012 L2b 362 + 31 | chr5 149448119 149448264 L3 215 - 32 | chr5 149448476 149448529 MIRc 213 + 33 | chr5 149448530 149448648 MIRb 428 + 34 | chr5 149449353 149449425 G-rich 207 + 35 | chr5 149450430 149450493 L3 195 - 36 | chr5 149450564 149450777 MIRb 567 + 37 | chr5 149450945 149450972 AT_rich 27 + 38 | chr5 149451119 149451291 Tigger15a 335 - 39 | chr5 149451562 149451669 MER117 394 + 40 | chr5 149451774 149452079 AluSq2 2383 + 41 | chr5 149452116 149452295 LTR85b 346 + 42 | chr5 149452574 149452698 LTR85b 405 + 43 | chr5 149452722 149452788 MIR3 249 - 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 | -------------------------------------------------------------------------------- /examples/annot/test1.wig: -------------------------------------------------------------------------------- 1 | fixedStep chrom=chr3 start=400601 step=100 2 | 11 3 | 22 4 | 33 5 | 33 6 | 333 7 | variableStep chrom=chrX start=9001 step=1 8 | 33 9 | 324 10 | 35334 11 | 34333 12 | 0 13 | 0 14 | 0 15 | -------------------------------------------------------------------------------- /examples/annot/test2.wig: -------------------------------------------------------------------------------- 1 | fixedStep chrom=chr3 start=400601 step=100 2 | 0 3 | 10 4 | 100 5 | 200 6 | 300 7 | 408 8 | 505 9 | 600 10 | 700 11 | 800 12 | 900 13 | 1000 14 | 975 15 | 700 16 | 652 17 | 410 18 | 100 19 | 74 20 | 0 21 | fixedStep chrom=chrX start=9001 step=1 span=2000 22 | 353 23 | 53 24 | 754 25 | 4333 26 | 0 27 | 0 -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /examples/nt-seq/test2.fa: -------------------------------------------------------------------------------- 1 | >SRR794330.25 2 | GGCTGCGCGGGCGCTGCGGCCGCACGGCGCGACTGTCCCCGGGCCGGGCA 3 | >SRR794330.34 4 | GGCTGCG--GGCGCTGCGGCCGCACGGCGCGACTGTCCCCGGGCCGGGCA 5 | >SRR794330.98 6 | AGCATCTGCGCGGGCGCTGCGGCCGCACGGCGCGACTGTCCCCGGGCCGG 7 | >SRR794330.123 8 | GGCTGCGCGGGCGCTGCGGCCGCACGNNNNNNNNGTCCCCGGGCCGGGCA 9 | -------------------------------------------------------------------------------- /examples/nt-seq/test2.fq: -------------------------------------------------------------------------------- 1 | @SRR794330.20 1101:2012:2162/1 2 | GCCTGTTCTTTCCACTAAATGAAACAACCTTAATAAAAATGCTGTTCT 3 | + 4 | @@@FFFFFHGHDHIJIJJJIIIIIJJJGIJJJJIJFIJJIIJJJGEHI 5 | @SRR794330.21 1101:2062:2165/1 6 | CCCAGGCTAACAAATGTCTATCAGGTACCCAACTAAAAACTAAAATCT 7 | + 8 | ##-+*''))**55CCF-->>>>CCCCCCC6DEHHHHJJJIJJJJJJJJ -------------------------------------------------------------------------------- /examples/nt-seq/test2.fq.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ababaian/bioSyntax-archive/4a86b38c2f348694786a066f275a0ede79d471af/examples/nt-seq/test2.fq.gz -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /examples/nt-seq/test_alignment2.clustal: -------------------------------------------------------------------------------- 1 | CLUSTAL W (1.82) multiple sequence alignment 2 | 3 | abc GCAUGCAUCUGCAUACGUACGUACGCAUGCAUCA 4 | def ---------------------------------- 5 | xyz ---------------------------------- 6 | 7 | abc GUCGAUACAUACGUACGUCGUACGUACGU-CGAC 8 | def ---------------CGCGAUGCAUGCAU-CGAU 9 | xyz -----------CAUGCAUCGUACGUACGCAUGAC 10 | -------------------------------------------------------------------------------- /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 | -------------------------------------------------------------------------------- /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/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 | -------------------------------------------------------------------------------- /examples/pdb/pdbx.link: -------------------------------------------------------------------------------- 1 | http://mmcif.wwpdb.org/ 2 | -------------------------------------------------------------------------------- /examples/sam/test.flagstat: -------------------------------------------------------------------------------- 1 | 1551234338 + 0 in total (QC-passed reads + QC-failed reads) 2 | 0 + 0 duplicates 3 | 951239 + 0 mapped (0.06%:-nan%) 4 | 1551234338 + 0 paired in sequencing 5 | 775617169 + 0 read1 6 | 775617169 + 0 read2 7 | 3904 + 0 properly paired (0.00%:-nan%) 8 | 9874 + 0 with itself and mate mapped 9 | 941365 + 0 singletons (0.06%:-nan%) 10 | 0 + 0 with mate mapped to a different chr 11 | 0 + 0 with mate mapped to a different chr (mapQ>=5) 12 | -------------------------------------------------------------------------------- /examples/vcf/test_1000genomes.vcf.gz: -------------------------------------------------------------------------------- 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-------------------------------------------------------------------------------- 1 | 2 | 13 | 14 | 15 | text/bed 16 | *.bed 17 | 18 | 19 | 20 |