├── .gitignore ├── LICENSE ├── README.md ├── example ├── example.fq ├── example.sam ├── example_dna.fa ├── example_protein.fa └── imgs │ ├── color_atla.png │ ├── emoji.png │ ├── simple.png │ ├── theme_glimpse │ ├── emoji │ │ ├── emoji-fq.png │ │ └── emoji-sam.png │ ├── simple │ │ ├── simple-fa.png │ │ ├── simple-fq.png │ │ └── simple-sam.png │ └── verbose │ │ ├── verbose-fq.png │ │ └── verbose-sam.png │ └── title.png ├── shell_config ├── bash_config.bash └── fish_config.fish ├── src ├── argparse.nim ├── color_atla.nim ├── configs.nim ├── fasta_utils.nim ├── fastq_utils.nim ├── main.nim └── sam_utils.nim ├── test.sh └── theme ├── README.md ├── emoji.json ├── simple.json └── verbose.json /.gitignore: -------------------------------------------------------------------------------- 1 | src/nimcache 2 | bin/ 3 | release/ -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | GNU GENERAL PUBLIC LICENSE 2 | Version 3, 29 June 2007 3 | 4 | Copyright (C) 2007 Free Software Foundation, Inc. 5 | Everyone is permitted to copy and distribute verbatim copies 6 | of this license document, but changing it is not allowed. 7 | 8 | Preamble 9 | 10 | The GNU General Public License is a free, copyleft license for 11 | software and other kinds of works. 12 | 13 | The licenses for most software and other practical works are designed 14 | to take away your freedom to share and change the works. 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It is safest 630 | to attach them to the start of each source file to most effectively 631 | state the exclusion of warranty; and each file should have at least 632 | the "copyright" line and a pointer to where the full notice is found. 633 | 634 | 635 | Copyright (C) 636 | 637 | This program is free software: you can redistribute it and/or modify 638 | it under the terms of the GNU General Public License as published by 639 | the Free Software Foundation, either version 3 of the License, or 640 | (at your option) any later version. 641 | 642 | This program is distributed in the hope that it will be useful, 643 | but WITHOUT ANY WARRANTY; without even the implied warranty of 644 | MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 645 | GNU General Public License for more details. 646 | 647 | You should have received a copy of the GNU General Public License 648 | along with this program. If not, see . 649 | 650 | Also add information on how to contact you by electronic and paper mail. 651 | 652 | If the program does terminal interaction, make it output a short 653 | notice like this when it starts in an interactive mode: 654 | 655 | Copyright (C) 656 | This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. 657 | This is free software, and you are welcome to redistribute it 658 | under certain conditions; type `show c' for details. 659 | 660 | The hypothetical commands `show w' and `show c' should show the appropriate 661 | parts of the General Public License. Of course, your program's commands 662 | might be different; for a GUI interface, you would use an "about box". 663 | 664 | You should also get your employer (if you work as a programmer) or school, 665 | if any, to sign a "copyright disclaimer" for the program, if necessary. 666 | For more information on this, and how to apply and follow the GNU GPL, see 667 | . 668 | 669 | The GNU General Public License does not permit incorporating your program 670 | into proprietary programs. If your program is a subroutine library, you 671 | may consider it more useful to permit linking proprietary applications with 672 | the library. If this is what you want to do, use the GNU Lesser General 673 | Public License instead of this License. But first, please read 674 | . -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # bioView 2 | 3 | A configurable and easy install command line tool for the readability enhancement of bioinformatic file format: fasta, fastq and sam file. 4 | 5 | ![title](./example/imgs/title.png) 6 | 7 | ## Installation 8 | 9 | This tools is writen in Nim, it can be compiled to a single excutable file. 10 | So, it is very easy to install, just download the [released](https://github.com/Nanguage/bioView/releases) excutable file, and add it to your PATH. 11 | 12 | ### Shell configuration 13 | 14 | For ease of use, you can append the configuration to your shell config file. 15 | 16 | * For Bash shell: [bash config](./shell_config/bash_config.bash) 17 | * For Fish shell: [fish config](./shell_config/fish_config.fish) 18 | 19 | ## Usage 20 | 21 | ``` 22 | Usage: 23 | bioview fq [--config-file=] [--hist=] [--color=] [--phred=<33/64>] [--delimiter=] 24 | bioview fa [--config-file=] [--color=] [--type=] 25 | bioview sam [--config-file=] [--hist=] [--color=] [--phred=<33/64>] [--multiline=] 26 | bioview color-atla 27 | bioview example-config 28 | bioview (-h | --help) 29 | ``` 30 | 31 | ### Example: 32 | 33 | View fastq file: 34 | 35 | ``` bash 36 | $ bioview fq example.fq | less -rS 37 | ``` 38 | 39 | View fasta file: 40 | 41 | ``` base 42 | $ bioview fa example_dna.fa | less -rS 43 | ``` 44 | 45 | View fasta file(protein record): 46 | 47 | ``` bash 48 | $ bioview fa example_protein.fa | less -rS 49 | ``` 50 | 51 | View sam file: 52 | 53 | ``` bash 54 | $ bioview sam example_sam.sam | less -rS 55 | ``` 56 | 57 | View sam file(multiline format): 58 | 59 | ``` bash 60 | $ bioview sam example_sam.sam --multiline | less -rS 61 | ``` 62 | 63 | Use '-' to read from stdin: 64 | 65 | ``` bash 66 | $ samtools view -h example.bam | bioview sam - | less -rS 67 | ``` 68 | 69 | ### bio-less 70 | 71 | Use the `bio-less` function defined in the [shell configuration](./shell_config/bash_config.bash), it let you use bioView more conveniently. 72 | 73 | ``` 74 | Usage: 75 | bio-less <*.fq/*.fa/*.sam/*.bam> 76 | fq-less <*.fq> 77 | fa-less <*.fa> 78 | sam-less <*.sam> 79 | ``` 80 | 81 | For example: 82 | 83 | ``` bash 84 | $ bio-less example.fq 85 | ``` 86 | 87 | This is equal to: `bioview fq example.fq | less -rS` 88 | 89 | ``` 90 | $ fq-less example.fq # equal to `bioview fq example.fq | less -rS` 91 | $ samtools view -h example.bam | sam-less - # equal to `samtools view -h example.bam | bioview sam - | less -rS` 92 | ``` 93 | 94 | ## Theme 95 | 96 | Provide different themes you can choise. 97 | 98 | ### simple (default) 99 | 100 | ### verbose 101 | 102 | ### emoji 103 | 104 | [see more](./theme/README.md). 105 | 106 | ## Make your own theme 107 | 108 | You can make your own theme through the config file. 109 | 110 | Just generate the config templete, and edit it: 111 | 112 | ``` bash 113 | $ mkdir -p ~/.config/bioview/config.json 114 | $ bioview example-config > ~/.config/bioview/config.json 115 | $ vim ~/.config/bioview/config.json 116 | ``` 117 | 118 | ### Color 119 | 120 | The `color` fields used to specify the color of related item, for example the `base color` denote the color of base(ATCG), 121 | and the `fq_config::hist::color` denote the color of histogram in the fastq view. The `fg` and `bg` field means the color 122 | code of the forground color and the background color. You can query the color code through the command: 123 | 124 | ``` bash 125 | $ bioview color-atla 126 | ``` 127 | 128 | It will list all supported forground color and background color. like: 129 | 130 | ![color-atla](./example/imgs/color_atla.png) 131 | 132 | And use the code `-1` denote the "non-color". 133 | 134 | ### Histogram 135 | 136 | The `fq_config::hist` and `sam_config::hist` fields used to specify the color and symbols of the histogram. 137 | 138 | default histogram symbols: 139 | ``` 140 | ▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████ 141 | ``` 142 | 143 | You can also use other symbols, like the emoji: 144 | ``` 145 | 👿👿👿👿👿😫😫😫😫😫🙁🙁🙁🙁🙁😣😣😣😣😣🙃🙃🙃🙃🙃😑😑😑😑😑🙂🙂🙂🙂🙂😃😃😃😃😃 146 | ``` 147 | 148 | For align histogram with the base correctly, you should specify the `hist::align` field. 149 | 150 | ## Development 151 | 152 | This project is written by [Nim](https://nim-lang.org/), and tested under unix-like system environment. 153 | You need [install Nim](https://nim-lang.org/install.html) firstly. 154 | 155 | ### Compile the code 156 | 157 | Compilation: 158 | 159 | ``` bash 160 | $ git clone https://github.com/Nanguage/bioView.git 161 | $ cd bioView 162 | $ mkdir bin 163 | $ nim c -d:release -o:./bin/bioview src/main.nim 164 | ``` 165 | 166 | Unit test: 167 | 168 | ``` bash 169 | $ ./test.sh # test all moudles 170 | $ ./test.sh fastq_utils # test the fastq_utils.nim moudle 171 | ``` 172 | ## TODO 173 | + upport other file format: 174 | * GTF/GFF 175 | * PDB 176 | * VCF 177 | * BED/BedGraph/BEDPE 178 | + Fix the color show bug with `less`. 179 | -------------------------------------------------------------------------------- /example/example_dna.fa: -------------------------------------------------------------------------------- 1 | >HSBGPG Human gene for bone gla protein (BGP) 2 | GGCAGATTCCCCCTAGACCCGCCCGCACCATGGTCAGGCATGCCCCTCCTCATCGCTGGGCACAGCCCAGAGGGT 3 | ATAAACAGTGCTGGAGGCTGGCGGGGCAGGCCAGCTGAGTCCTGAGCAGCAGCCCAGCGCAGCCACCGAGACACC 4 | ATGAGAGCCCTCACACTCCTCGCCCTATTGGCCCTGGCCGCACTTTGCATCGCTGGCCAGGCAGGTGAGTGCCCC 5 | CACCTCCCCTCAGGCCGCATTGCAGTGGGGGCTGAGAGGAGGAAGCACCATGGCCCACCTCTTCTCACCCCTTTG 6 | GCTGGCAGTCCCTTTGCAGTCTAACCACCTTGTTGCAGGCTCAATCCATTTGCCCCAGCTCTGCCCTTGCAGAGG 7 | GAGAGGAGGGAAGAGCAAGCTGCCCGAGACGCAGGGGAAGGAGGATGAGGGCCCTGGGGATGAGCTGGGGTGAAC 8 | CAGGCTCCCTTTCCTTTGCAGGTGCGAAGCCCAGCGGTGCAGAGTCCAGCAAAGGTGCAGGTATGAGGATGGACC 9 | TGATGGGTTCCTGGACCCTCCCCTCTCACCCTGGTCCCTCAGTCTCATTCCCCCACTCCTGCCACCTCCTGTCTG 10 | GCCATCAGGAAGGCCAGCCTGCTCCCCACCTGATCCTCCCAAACCCAGAGCCACCTGATGCCTGCCCCTCTGCTC 11 | CACAGCCTTTGTGTCCAAGCAGGAGGGCAGCGAGGTAGTGAAGAGACCCAGGCGCTACCTGTATCAATGGCTGGG 12 | GTGAGAGAAAAGGCAGAGCTGGGCCAAGGCCCTGCCTCTCCGGGATGGTCTGTGGGGGAGCTGCAGCAGGGAGTG 13 | GCCTCTCTGGGTTGTGGTGGGGGTACAGGCAGCCTGCCCTGGTGGGCACCCTGGAGCCCCATGTGTAGGGAGAGG 14 | AGGGATGGGCATTTTGCACGGGGGCTGATGCCACCACGTCGGGTGTCTCAGAGCCCCAGTCCCCTACCCGGATCC 15 | CCTGGAGCCCAGGAGGGAGGTGTGTGAGCTCAATCCGGACTGTGACGAGTTGGCTGACCACATCGGCTTTCAGGA 16 | GGCCTATCGGCGCTTCTACGGCCCGGTCTAGGGTGTCGCTCTGCTGGCCTGGCCGGCAACCCCAGTTCTGCTCCT 17 | CTCCAGGCACCCTTCTTTCCTCTTCCCCTTGCCCTTGCCCTGACCTCCCAGCCCTATGGATGTGGGGTCCCCATC 18 | ATCCCAGCTGCTCCCAAATAAACTCCAGAAG 19 | >HSGLTH1 Human theta 1-globin gene 20 | ccactgcactcaccgcacccggccaatttttgtgtttttagtagagactaaataccatatagtgaacacctaaga 21 | cggggggccttggatccagggcgattcagagggccccggtcggagctgtcggagattgagcgcgcgcggtcccgg 22 | gatctccgacgaggccctggacccccgggcggcgaagctgcggcgcggcgccccctggaggccgcgggacccctg 23 | gccggtccgcgcaggcgcagcggggtcgcagggcgcggcgggttccagcgcggggatggcgctgtccgcggagga 24 | ccgggcgctggtgcgcgccctgtggaagaagctgggcagcaacgtcggcgtctacacgacagaggccctggaaag 25 | gtgcggcaggctgggcgcccccgcccccaggggccctccctccccaagccccccggacgcgcctcacccacgttc 26 | ctctcgcaggaccttcctggctttccccgccacgaagacctacttctcccacctggacctgagccccggctcctc 27 | acaagtcagagcccacggccagaaggtggcggacgcgctgagcctcgccgtggagcgcctggacgacctacccca 28 | cgcgctgtccgcgctgagccacctgcacgcgtgccagctgcgagtggacccggccagcttccaggtgagcggctg 29 | ccgtgctgggcccctgtccccgggagggccccggcggggtgggtgcggggggcgtgcggggcgggtgcaggcgag 30 | tgagccttgagcgctcgccgcagctcctgggccactgcctgctggtaaccctcgcccggcactaccccggagact 31 | tcagccccgcgctgcaggcgtcgctggacaagttcctgagccacgttatctcggcgctggtttccgagtaccgct 32 | gaactgtgggtgggtggccgcgggatccccaggcgaccttccccgtgtttgagtaaagcctctcccaggagcagc 33 | cttcttgccgtgctctctcgaggtcaggacgcgagaggaaggcgc -------------------------------------------------------------------------------- /example/example_protein.fa: -------------------------------------------------------------------------------- 1 | >SEQUENCE_1 2 | MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG 3 | LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK 4 | IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL 5 | MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL 6 | >SEQUENCE_2 7 | SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI 8 | ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH 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export PATH="/path/to/bioview/:$PATH" 2 | 3 | function bio-less { 4 | file=$1 5 | 6 | if [[ $file == *.fq ]]; then 7 | bioview fq $file ${@:2} | less -rS 8 | elif [[ $file == *.fa ]]; then 9 | bioview fa $file ${@:2} | less -rS 10 | elif [[ $file == *.sam ]]; then 11 | bioview sam $file ${@:2} | less -rS 12 | elif [[ $file == *.bam ]]; then 13 | samtools view -h $file | bioview sam - ${@:2} | less -rS 14 | else 15 | less -S $file 16 | fi 17 | 18 | } 19 | 20 | function fq-less { 21 | bioview fq $@ | less -rS 22 | } 23 | 24 | function fa-less { 25 | bioview fa $@ | less -rS 26 | } 27 | 28 | function sam-less { 29 | bioview sam $@ | less -rS 30 | } -------------------------------------------------------------------------------- /shell_config/fish_config.fish: -------------------------------------------------------------------------------- 1 | set PATH /path/to/bioview $PATH 2 | 3 | function bio-less 4 | set file $argv[1] 5 | set --erase argv[1] 6 | 7 | switch $file 8 | case "*.fq" 9 | bioview fq $file $argv | less -rS 10 | case "*.fa" 11 | bioview fa $file $argv | less -rS 12 | case "*.sam" 13 | bioview sam $file $argv | less -rS 14 | case "*.bam" 15 | samtools view -h $file | bioview sam - $argv | less -rS 16 | case "*" 17 | less -S $file 18 | end 19 | end 20 | 21 | function fq-less 22 | bioview fq $argv | less -rS 23 | end 24 | 25 | function fa-less 26 | bioview fa $argv | less -rS 27 | end 28 | 29 | function sam-less 30 | bioview sam $argv | less -rS 31 | end -------------------------------------------------------------------------------- /src/argparse.nim: -------------------------------------------------------------------------------- 1 | import tables 2 | import parseopt 3 | 4 | type 5 | 6 | ValueKind* = enum 7 | vkNone, 8 | vkBool, 9 | vkStr, 10 | 11 | Value* = object 12 | case kind*: ValueKind 13 | of vkNone: 14 | nil 15 | of vkBool: 16 | bool_v: bool 17 | of vkStr: 18 | str_v: string 19 | 20 | 21 | converter to_bool*(v: Value): bool = 22 | case v.kind 23 | of vkNone: 24 | false 25 | of vkBool: 26 | v.bool_v 27 | of vkStr: 28 | v.str_v != "" and v.str_v.len > 0 29 | 30 | 31 | proc val(): Value = Value(kind: vkNone) 32 | proc val(v: bool): Value = Value(kind: vkBool, bool_v: v) 33 | proc val(v: string): Value = Value(kind: vkStr, str_v: v) 34 | 35 | 36 | proc `$`*(v: Value): string = 37 | case v.kind 38 | of vkNone: 39 | "nil" 40 | of vkBool: 41 | $v.bool_v 42 | of vkStr: 43 | v.str_v 44 | 45 | 46 | proc parse_args*(doc: string): Table[string, Value] = 47 | 48 | result = { 49 | "fq": val(), 50 | "fa": val(), 51 | "sam": val(), 52 | "": val(), 53 | "color-atla": val(), 54 | "example-config": val(), 55 | 56 | "--phred": val(), 57 | "--hist": val(), 58 | "--delimiter": val(), 59 | "--multiline": val(), 60 | "--color": val(), 61 | "--type": val(), 62 | "--config-file": val(), 63 | }.toTable() 64 | 65 | var arg_ct: int = 0 66 | 67 | for kind, key, value in getopt(): 68 | when not defined(release): 69 | stderr.write(($kind) & " " & ($key) & " " & ($value) & "\n") 70 | stderr.flushFile() 71 | case kind 72 | of cmdArgument: 73 | case arg_ct: 74 | of 0: 75 | case key: 76 | of "fq": 77 | result["fq"] = val(true) 78 | of "fa": 79 | result["fa"] = val(true) 80 | of "sam": 81 | result["sam"] = val(true) 82 | of "color-atla": 83 | result["color-atla"] = val(true) 84 | return result 85 | of "example-config": 86 | result["example-config"] = val(true) 87 | return result 88 | of 1: 89 | result[""] = val(key) 90 | else: 91 | echo doc 92 | quit(1) 93 | inc arg_ct 94 | of cmdShortOption: 95 | case key 96 | of "h": 97 | echo doc 98 | quit(0) 99 | if key == "" and value == "": 100 | result[""] = val("-") 101 | inc arg_ct 102 | of cmdLongOption: 103 | case key: 104 | of "h", "help": 105 | echo doc 106 | quit(0) 107 | of "phred": 108 | result["--phred"] = val(value) 109 | of "hist": 110 | result["--hist"] = val(value) 111 | of "delimiter": 112 | result["--delimiter"] = val(value) 113 | of "multiline": 114 | if value != "": 115 | result["--multiline"] = val(value) 116 | else: 117 | result["--multiline"] = val("yes") 118 | of "color": 119 | result["--color"] = val(value) 120 | of "type": 121 | result["--type"] = val(value) 122 | of "config-file": 123 | result["--config-file"] = val(value) 124 | of cmdEnd: 125 | discard 126 | 127 | if (not result["fq"]) and (not result["fa"]) and (not result["sam"]) and 128 | (not result["example-config"]) and (not result["color-atla"]): 129 | echo doc 130 | quit(1) 131 | 132 | 133 | when isMainModule: 134 | discard -------------------------------------------------------------------------------- /src/color_atla.nim: -------------------------------------------------------------------------------- 1 | import tables 2 | import strutils 3 | 4 | type 5 | Color* = ref object 6 | fg*: int 7 | bg*: int 8 | 9 | ValColor* = ref object 10 | val*: int 11 | color*: Color 12 | 13 | ColorRange* = ref object 14 | buttom*: ValColor 15 | top*: ValColor 16 | 17 | BaseColor* = ref object 18 | A*: Color 19 | T*: Color 20 | C*: Color 21 | G*: Color 22 | U*: Color 23 | N*: Color 24 | 25 | AminoColor* = ref object 26 | A*: Color 27 | R*: Color 28 | N*: Color 29 | D*: Color 30 | C*: Color 31 | E*: Color 32 | Q*: Color 33 | G*: Color 34 | H*: Color 35 | I*: Color 36 | L*: Color 37 | K*: Color 38 | M*: Color 39 | F*: Color 40 | P*: Color 41 | S*: Color 42 | T*: Color 43 | W*: Color 44 | Y*: Color 45 | V*: Color 46 | 47 | FqIdPartsColors* = ref object 48 | instrument*: Color 49 | run_id*: Color 50 | flowcell_id*: Color 51 | tile_number*: Color 52 | x_coordinate*: Color 53 | y_coordinate*: Color 54 | pair*: Color 55 | filtered*: Color 56 | control_bits*: Color 57 | index_seq*: Color 58 | 59 | 60 | proc toTable(base_color: BaseColor): Table[char, Color] = 61 | result = { 62 | 'A': base_color.A, 63 | 'T': base_color.T, 64 | 'C': base_color.C, 65 | 'G': base_color.G, 66 | 'U': base_color.U, 67 | 'N': base_color.N, 68 | }.toTable() 69 | 70 | 71 | proc toTable(amino_color: AminoColor): Table[char, Color] = 72 | result = { 73 | 'A': amino_color.A, 74 | 'R': amino_color.R, 75 | 'N': amino_color.N, 76 | 'D': amino_color.D, 77 | 'C': amino_color.C, 78 | 'E': amino_color.E, 79 | 'Q': amino_color.Q, 80 | 'G': amino_color.G, 81 | 'H': amino_color.H, 82 | 'I': amino_color.I, 83 | 'L': amino_color.L, 84 | 'K': amino_color.K, 85 | 'M': amino_color.M, 86 | 'F': amino_color.F, 87 | 'P': amino_color.P, 88 | 'S': amino_color.S, 89 | 'T': amino_color.T, 90 | 'W': amino_color.W, 91 | 'Y': amino_color.Y, 92 | 'V': amino_color.V, 93 | }.toTable() 94 | 95 | 96 | proc colorize*(str_in:string|char, color:Color): string = 97 | if color.fg < 0 and color.bg >= 0: 98 | result = "\e[48;5;" & $color.bg & "m" & str_in & "\e[0m" 99 | elif color.fg >= 0 and color.bg < 0: 100 | result = "\e[38;5;" & $color.fg & "m" & str_in & "\e[0m" 101 | elif color.fg >= 0 and color.bg >= 0: 102 | result = "\e[38;5;" & $color.fg & "m" & "\e[48;5;" & $color.bg & "m" & str_in & "\e[0m" 103 | else: 104 | result = $str_in 105 | 106 | 107 | proc colorize*(str_in:string|char, color_fg, color_bg: int): string = 108 | result = "\e[38;5;" & $color_fg & "m" & "\e[48;5;" & $color_bg & "m" & str_in & "\e[0m" 109 | 110 | 111 | proc colorize*(str_in:string|char, color_fg: int): string = 112 | result = "\e[38;5;" & $color_fg & "m" & str_in & "\e[0m" 113 | 114 | 115 | proc colorize*(str_in:string|char, color_bg: int): string = 116 | result = "\e[48;5;" & $color_bg & "m" & str_in & "\e[0m" 117 | 118 | 119 | proc colorize_seq*(seq_str:string, color:BaseColor|AminoColor): string = 120 | result = "" 121 | var colored: string 122 | let color_map: Table[char, Color] = color.toTable() 123 | var char_set:set[char] = {} 124 | for c in color_map.keys(): 125 | char_set.incl(c) 126 | 127 | for base in seq_str: 128 | if base.toUpperAscii() in char_set: 129 | let color = color_map[base.toUpperAscii()] 130 | colored = base.colorize(color) 131 | else: 132 | colored = $base 133 | result.add(colored) 134 | 135 | 136 | proc determine_color(score:int, color_low:int, val_low:int, color_high:int, val_high:int): int = 137 | # determine foreground or background color 138 | if color_low == color_high or val_low == val_high: 139 | return color_low 140 | elif color_low < color_high: 141 | if score < val_low: 142 | return color_low 143 | elif score > val_high: 144 | return color_high 145 | let r:float = (score - val_low) / (val_high - val_low) 146 | let color = (color_low.float + (color_high - color_low).float * r).int 147 | return color 148 | else: 149 | if score > val_high: 150 | return color_high 151 | elif score < val_low: 152 | return color_low 153 | let r:float = (score - val_low) / (val_high - val_low) 154 | let color = (color_high.float + (color_low - color_high).float * r).int 155 | return color 156 | 157 | 158 | proc colorize_score*(score:int, color_range:ColorRange): string = 159 | let cr = color_range 160 | 161 | doAssert(cr.buttom.val <= cr.top.val) 162 | let val_range = (cr.buttom.val, cr.top.val) 163 | 164 | let fg = determine_color(score, cr.buttom.color.fg, val_range[0], cr.top.color.fg, val_range[1]) 165 | let bg = determine_color(score, cr.buttom.color.bg, val_range[0], cr.top.color.bg, val_range[1]) 166 | 167 | result = colorize(score.intToStr, Color(fg:fg, bg:bg)) 168 | 169 | 170 | proc print_color_atla*(num_per_line:int=10) = 171 | #[ 172 | print color atla to console. 173 | ]# 174 | proc print_colors(fgbg:string) = 175 | var color_block: string 176 | for color in 0..255: 177 | if fgbg == "fg": 178 | color_block = (" " & ($color).align(3) & " ").colorize(color_fg=color) 179 | else: 180 | color_block = (" " & ($color).align(3) & " ").colorize(color_bg=color) 181 | stdout.write(color_block) 182 | if (color + 1) %% num_per_line == 0: 183 | stdout.write("\n") 184 | stdout.write("\n") 185 | 186 | echo("Color code:") 187 | echo() 188 | echo("Forground:".colorize(color_fg=16, color_bg=255)) 189 | print_colors(fgbg="fg") 190 | echo() 191 | echo("Background:".colorize(color_fg=16, color_bg=255)) 192 | print_colors(fgbg="bg") 193 | 194 | 195 | when isMainModule: 196 | let s1 = "attggc" 197 | var c1 = Color(fg:56, bg:(-1)) 198 | 199 | echo s1.colorize(c1) 200 | 201 | c1.fg = -1 202 | echo s1.colorize(c1) 203 | 204 | c1.fg = -1 205 | c1.bg = 30 206 | echo s1.colorize(c1) 207 | 208 | c1.fg = 10 209 | c1.bg = 20 210 | echo s1.colorize(c1) 211 | 212 | echo $determine_color(20, 232, 0, 255, 30) 213 | 214 | import configs 215 | let config = load_config() 216 | echo colorize_score(20, config.sam_config.mapq_color_range) -------------------------------------------------------------------------------- /src/configs.nim: -------------------------------------------------------------------------------- 1 | import os 2 | import json 3 | import unicode 4 | 5 | import color_atla 6 | 7 | type 8 | FqIdentifier* = ref object 9 | color*: Color 10 | parse_parts*: bool 11 | parts_colors*: FqIdPartsColors 12 | 13 | Hist* = ref object 14 | use*: bool 15 | symbols*: string 16 | symbol_unit_len*: int 17 | align*: int 18 | color*: Color 19 | 20 | Delimiter* = ref object 21 | use*: bool 22 | str*: string 23 | len*: int 24 | color*: Color 25 | 26 | FastqConfig* = ref object 27 | phred*: int 28 | use_color*: bool 29 | use_base_color*: bool 30 | hist*: Hist 31 | identifier*: FqIdentifier 32 | delimiter*: Delimiter 33 | 34 | FastaConfig* = ref object 35 | use_color*: bool 36 | use_base_color*: bool 37 | record_type*: string 38 | amino_color*: AminoColor 39 | identifier_color*: Color 40 | 41 | SamHeader* = ref object 42 | header_type*: Color 43 | item_key*: Color 44 | item_value*: Color 45 | 46 | SamOptionalFields* = ref object 47 | tag*: Color 48 | field_type*: Color 49 | value*: Color 50 | 51 | SamConfig* = ref object 52 | phred*: int 53 | multiline*: bool 54 | delimiter*: Delimiter 55 | use_color*: bool 56 | header_color*: SamHeader 57 | qname_color*: Color 58 | flag_color*: Color 59 | rname_color*: Color 60 | pos_color*: Color 61 | mapq_color_range*: ColorRange 62 | cigar_color*: Color 63 | rnext_color*: Color 64 | pnext_color*: Color 65 | tlen_color*: Color 66 | use_base_color*: bool 67 | hist*: Hist 68 | optional_fields_color*: SamOptionalFields 69 | 70 | Config* = ref object 71 | base_color*: BaseColor 72 | fq_config*: FastqConfig 73 | fa_config*: FastaConfig 74 | sam_config*: SamConfig 75 | 76 | 77 | let default_json_str* = """ 78 | { 79 | "base_color": 80 | { 81 | "A": {"fg": 196, "bg": -1}, 82 | "T": {"fg": 50 , "bg": -1}, 83 | "C": {"fg": 226, "bg": -1}, 84 | "G": {"fg": 82 , "bg": -1}, 85 | "U": {"fg": -1, "bg": -1}, 86 | "N": {"fg": -1, "bg": -1} 87 | }, 88 | 89 | "fq_config": 90 | { 91 | "phred": 33, 92 | 93 | "use_color": true, 94 | "use_base_color": true, 95 | 96 | "hist": { 97 | "use": true, 98 | "symbols": 99 | "▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████", 100 | "symbol_unit_len": 3, 101 | "align": 1, 102 | "color": {"fg": -1, "bg": -1} 103 | }, 104 | 105 | "identifier": { 106 | "color": {"fg": -1, "bg": -1}, 107 | "parse_parts": false, 108 | "parts_colors": { 109 | "instrument": {"fg": -1, "bg": -1}, 110 | "run_id": {"fg": -1, "bg": -1}, 111 | "flowcell_id": {"fg": -1, "bg": -1}, 112 | "tile_number": {"fg": -1, "bg": -1}, 113 | "x_coordinate": {"fg": -1, "bg": -1}, 114 | "y_coordinate": {"fg": -1, "bg": -1}, 115 | "pair": {"fg": -1, "bg": -1}, 116 | "filtered": {"fg": -1, "bg": -1}, 117 | "control_bits": {"fg": -1, "bg": -1}, 118 | "index_seq": {"fg": -1, "bg": -1} 119 | } 120 | }, 121 | 122 | "delimiter": { 123 | "use": true, 124 | "str": "-", 125 | "len": 150, 126 | "color": {"fg": -1, "bg": -1} 127 | } 128 | 129 | }, 130 | 131 | "fa_config": 132 | { 133 | "use_color": true, 134 | "use_base_color": true, 135 | 136 | "record_type": "dna", 137 | 138 | "amino_color": { 139 | "A": {"fg": 1, "bg": -1}, 140 | "R": {"fg": 2, "bg": -1}, 141 | "N": {"fg": 3, "bg": -1}, 142 | "D": {"fg": 4, "bg": -1}, 143 | "C": {"fg": 5, "bg": -1}, 144 | "E": {"fg": 6, "bg": -1}, 145 | "Q": {"fg": 7, "bg": -1}, 146 | "G": {"fg": 8, "bg": -1}, 147 | "H": {"fg": 9, "bg": -1}, 148 | "I": {"fg": 10, "bg": -1}, 149 | "L": {"fg": 11, "bg": -1}, 150 | "K": {"fg": 12, "bg": -1}, 151 | "M": {"fg": 13, "bg": -1}, 152 | "F": {"fg": 14, "bg": -1}, 153 | "P": {"fg": 15, "bg": -1}, 154 | "S": {"fg": 16, "bg": -1}, 155 | "T": {"fg": 17, "bg": -1}, 156 | "W": {"fg": 18, "bg": -1}, 157 | "Y": {"fg": 19, "bg": -1}, 158 | "V": {"fg": 20, "bg": -1} 159 | }, 160 | 161 | "identifier_color": {"fg": -1, "bg": -1} 162 | }, 163 | 164 | "sam_config": 165 | { 166 | "phred": 33, 167 | 168 | "use_color": true, 169 | 170 | "multiline": false, 171 | 172 | "delimiter": { 173 | "use": false, 174 | "str": "-", 175 | "len": 150, 176 | "color": {"fg": -1, "bg": -1} 177 | }, 178 | 179 | "header_color": { 180 | "header_type": {"fg": 111, "bg": -1}, 181 | "item_key": {"fg": 201, "bg": -1}, 182 | "item_value": {"fg": 202, "bg": -1} 183 | }, 184 | 185 | "qname_color": {"fg": 40, "bg": -1}, 186 | "flag_color": {"fg": 196, "bg": -1}, 187 | "rname_color": {"fg": 184, "bg": -1}, 188 | "pos_color": {"fg": 122, "bg": -1}, 189 | 190 | "mapq_color_range": { 191 | "buttom": {"val": 0, "color": {"fg": -1, "bg": 232}}, 192 | "top": {"val": 30, "color": {"fg": -1, "bg": 255}} 193 | }, 194 | 195 | "cigar_color": {"fg": 225, "bg": -1}, 196 | "rnext_color": {"fg": 63, "bg": -1}, 197 | "pnext_color": {"fg": 64, "bg": -1}, 198 | "tlen_color": {"fg": 200, "bg": -1}, 199 | 200 | "optional_fields_color": { 201 | "tag": {"fg": 14, "bg": -1}, 202 | "field_type": {"fg": 134, "bg": -1}, 203 | "value": {"fg": 210, "bg": -1} 204 | }, 205 | 206 | "use_base_color": true, 207 | 208 | "hist": { 209 | "use": true, 210 | "symbols": 211 | "▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████", 212 | "symbol_unit_len": 3, 213 | "align": 1, 214 | "color": {"fg": -1, "bg": -1} 215 | } 216 | 217 | } 218 | } 219 | """ 220 | 221 | 222 | proc example_json*() = 223 | echo(default_json_str) 224 | 225 | 226 | proc load_from_path(path: string="~/.config/bioview/config.json"): JsonNode = 227 | parseFile(path) 228 | 229 | 230 | proc load_config*(path: string=""): Config = 231 | var config_json: JsonNode 232 | if path != "" and existsFile(path): 233 | config_json = load_from_path(path) 234 | else: 235 | config_json = parseJson(default_json_str) 236 | 237 | result = to(config_json, Config) 238 | 239 | 240 | when isMainModule: 241 | # unit tests 242 | 243 | echo("example config json:") 244 | example_json() 245 | 246 | let config = load_config() 247 | 248 | let a_color_fg: int = config.base_color.A.fg 249 | doAssert(a_color_fg == 196) 250 | 251 | let a_color_bg: int = config.base_color.A.bg 252 | doAssert(a_color_bg == -1) 253 | 254 | let hist_symbols: string = config.fq_config.hist.symbols 255 | doAssert(hist_symbols.len() / 3 == 44) -------------------------------------------------------------------------------- /src/fasta_utils.nim: -------------------------------------------------------------------------------- 1 | import strutils 2 | 3 | from color_atla import colorize, colorize_seq 4 | from configs import Config 5 | 6 | proc process_fasta*(fname:string, config:Config) = 7 | let record_type = config.fa_config.record_type 8 | 9 | let use_color = config.fa_config.use_color 10 | let use_base_color = config.fa_config.use_base_color 11 | let id_color = config.fa_config.identifier_color 12 | let base_color = config.base_color 13 | let amino_color = config.fa_config.amino_color 14 | 15 | var f: File 16 | if fname == "-": 17 | f = stdin 18 | else: 19 | if open(f, fname): 20 | discard 21 | else: 22 | raise newException(IOError, fname & " can not open.") 23 | 24 | for line in f.lines: 25 | if line.startsWith('>'): # identifier line 26 | if use_color: 27 | echo line.colorize(id_color) 28 | else: 29 | echo line 30 | else: 31 | if use_color and use_base_color: 32 | let colored = 33 | if record_type.toUpperAscii == "PROTEIN": 34 | line.colorize_seq(amino_color) 35 | else: 36 | line.colorize_seq(base_color) 37 | echo colored 38 | else: 39 | echo line 40 | 41 | when isMainModule: 42 | discard 43 | -------------------------------------------------------------------------------- /src/fastq_utils.nim: -------------------------------------------------------------------------------- 1 | import strutils 2 | 3 | from color_atla import colorize, colorize_seq 4 | from color_atla import Color, BaseColor, FqIdPartsColors 5 | from configs import Config, Delimiter 6 | 7 | proc parse_quality*(quality_string:string, phred:int=33): seq[int] = 8 | assert phred == 33 or phred == 64 9 | result = @[] 10 | var q: int 11 | for c in quality_string: 12 | q = ord(c) - phred 13 | result.add(q) 14 | 15 | 16 | proc encode_quality*(quality:seq[int], phred:int=33): string = 17 | assert phred == 33 or phred == 64 18 | result = "" 19 | var c: char 20 | for q in quality: 21 | c = chr(q + phred) 22 | result.add(c) 23 | 24 | 25 | proc to_hist*(quality:seq[int], hist_symbols:string, symbol_unit_len:int=3): string = 26 | result = "" 27 | let slen = symbol_unit_len 28 | for q in quality: 29 | let s: int = ord(q) * slen 30 | let e: int = s + slen - 1 31 | if s < 0: 32 | result.add(hist_symbols[0.. hist_symbols.len: 34 | result.add(hist_symbols[hist_symbols.len-slen ..< hist_symbols.len]) 35 | else: 36 | result.add(hist_symbols[s..e]) 37 | 38 | 39 | proc add_space*(str:string, unit:int=1, space:int=1): string = 40 | result = "" 41 | var i: int = 1 42 | while i <= str.len: 43 | result.add(str[i-1]) 44 | if i mod unit == 0: 45 | result.add(" ".repeat(space)) 46 | inc i 47 | 48 | 49 | type 50 | Identifier = ref object 51 | instrument: string 52 | run_id: string 53 | flowcell_id: string 54 | tile_number: string 55 | x_coordinate: string 56 | y_coordinate: string 57 | pair: string 58 | filtered: string 59 | control_bits: string 60 | index_seq: string 61 | 62 | 63 | proc parse_identifier(name: string): Identifier = 64 | try: 65 | let names = name.split(' ') 66 | let (name1, name2) = (names[0], names[1]) 67 | let part1 = name1.split(':') 68 | let part2 = name2.split(':') 69 | result = Identifier( 70 | instrument: part1[0], 71 | run_id: part1[1], 72 | flowcell_id: part1[2], 73 | tile_number: part1[3], 74 | x_coordinate: part1[4], 75 | y_coordinate: part1[5], 76 | pair: part2[0], 77 | filtered: part2[1], 78 | control_bits: part2[2], 79 | index_seq: part2[3], 80 | ) 81 | except: 82 | result = nil 83 | 84 | 85 | proc to_string(id:Identifier, color:FqIdPartsColors): string = 86 | result = 87 | id.instrument.colorize(color.instrument) & ":" & 88 | id.run_id.colorize(color.run_id) & ":" & 89 | id.flowcell_id.colorize(color.flowcell_id) & ":" & 90 | id.tile_number.colorize(color.tile_number) & ":" & 91 | id.x_coordinate.colorize(color.x_coordinate) & ":" & 92 | id.y_coordinate.colorize(color.y_coordinate) & 93 | " " & 94 | id.pair.colorize(color.pair) & ":" & 95 | id.filtered.colorize(color.filtered) & ":" & 96 | id.control_bits.colorize(color.control_bits) & ":" & 97 | id.index_seq.colorize(color.index_seq) 98 | 99 | 100 | type 101 | FastqRecord = object 102 | name: string 103 | sequence: string 104 | quality: seq[int] 105 | 106 | 107 | proc to_string(self:FastqRecord, 108 | phred:int=33, 109 | use_color:bool=true, 110 | hist_symbols:string="", 111 | hist_symbol_unit_len:int=3, 112 | align:int=1, 113 | hist_color:Color=nil, 114 | base_color: BaseColor=nil, 115 | id_color: Color=nil, 116 | parts_colors: FqIdPartsColors=nil): string = 117 | var id_str: string 118 | var qua_str: string 119 | var seq_str: string 120 | 121 | # process identifier 122 | if parts_colors == nil: 123 | id_str = 124 | if use_color and id_color != nil: 125 | self.name.colorize(id_color) 126 | else: 127 | self.name 128 | else: 129 | let id = self.name.parse_identifier() 130 | if id != nil and use_color: 131 | id_str = id.to_string(parts_colors) 132 | else: 133 | # not use color or 134 | # exception occured when parse name to identifier 135 | id_str = self.name 136 | 137 | # process sequence 138 | seq_str = 139 | if align > 1: # align sequence 140 | self.sequence.add_space(unit=1, space=(align-1)) 141 | else: 142 | self.sequence 143 | 144 | if use_color and base_color != nil: # colorize sequence 145 | seq_str = seq_str.colorize_seq(base_color) 146 | else: 147 | seq_str = seq_str 148 | 149 | # process quality string 150 | if hist_symbols == "": 151 | qua_str = self.quality.encode_quality(phred=phred) 152 | else: # use histogram 153 | qua_str = self.quality.to_hist(hist_symbols, symbol_unit_len=hist_symbol_unit_len) 154 | if align > 1: # align quality string 155 | qua_str = qua_str.add_space(unit=hist_symbol_unit_len, space=(align-1)) 156 | if use_color and hist_color != nil: # colorize quality string 157 | qua_str = qua_str.colorize(color=hist_color) 158 | 159 | result = "@" & id_str & "\n" & 160 | seq_str & "\n" & 161 | "+\n" & 162 | qua_str 163 | 164 | 165 | iterator read_fastq(file:File, phred:int=33): FastqRecord = 166 | var rec = FastqRecord(name: "", sequence: "", quality: @[]) 167 | var line_num = 0 168 | for line in file.lines: 169 | inc line_num 170 | let i = (line_num) %% 4 171 | case i: 172 | of 1: 173 | rec.name = line[1..(line.len-1)] 174 | of 2: 175 | rec.sequence = line 176 | of 3: 177 | continue 178 | else: 179 | rec.quality = line.parse_quality(phred=phred) 180 | yield rec 181 | rec = FastqRecord(name: "", sequence: "", quality: @[]) 182 | 183 | 184 | proc to_string*(delimiter: Delimiter): string = 185 | result = delimiter.str.repeat(delimiter.len).colorize(delimiter.color) 186 | 187 | 188 | proc process_fastq*(fname: string, config:Config) = 189 | let phred = config.fq_config.phred 190 | if phred != 33 and phred != 64: 191 | raise newException(ValueError, "phred encode must be 33 or 64") 192 | let use_color = config.fq_config.use_color 193 | let base_color = if use_color: config.base_color else: nil 194 | 195 | let use_hist = config.fq_config.hist.use 196 | let hist_symbols = if use_hist: config.fq_config.hist.symbols else: "" 197 | let hist_color = config.fq_config.hist.color 198 | let hist_symbol_unit_len = config.fq_config.hist.symbol_unit_len 199 | let align = config.fq_config.hist.align 200 | 201 | let use_delimiter = config.fq_config.delimiter.use 202 | let delimiter = config.fq_config.delimiter 203 | 204 | let id_color = config.fq_config.identifier.color 205 | let parse_parts = config.fq_config.identifier.parse_parts 206 | let parts_colors = if parse_parts == false: nil else: config.fq_config.identifier.parts_colors 207 | 208 | var f: File 209 | if fname == "-": 210 | f = stdin 211 | else: 212 | if open(f, fname): 213 | discard 214 | else: 215 | raise newException(IOError, fname & " can not open.") 216 | 217 | if use_delimiter: 218 | echo delimiter.to_string() 219 | for rec in read_fastq(f, phred=phred): 220 | echo rec.to_string( 221 | hist_symbols=hist_symbols, hist_color=hist_color, hist_symbol_unit_len=hist_symbol_unit_len, align=align, 222 | use_color=use_color, base_color=base_color, phred=phred, 223 | id_color=id_color, parts_colors=parts_colors) 224 | if use_delimiter: 225 | echo delimiter.to_string() 226 | 227 | 228 | when isMainModule: 229 | import configs 230 | 231 | let config = configs.load_config() 232 | 233 | let qua_str_1 = "-AAFFJJJJJJJJJJJJJJJJFJJJFJJJJJJJFJJJJJJJJJJJJFJJJJJ" 234 | echo qua_str_1 235 | 236 | let qua_1 = qua_str_1.parse_quality() 237 | echo $qua_1 238 | doAssert(qua_1.len() == qua_str_1.len()) 239 | doAssert(qua_1.encode_quality() == qua_str_1) 240 | 241 | let symbols_1 = "▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████" 242 | let qua_1_hist = qua_1.to_hist(symbols_1) 243 | echo qua_1_hist 244 | doAssert(qua_str_1.len() == int(qua_1_hist.len() / 3)) 245 | 246 | echo qua_str_1.add_space(space=1) 247 | let symbols_2 = "👿👿👿👿👿😫😫😫😫😫🙁🙁🙁🙁🙁😣😣😣😣😣🙃🙃🙃🙃🙃😑😑😑😑😑🙂🙂🙂🙂🙂😃😃😃😃😃" 248 | let qua_2_hist = qua_1.to_hist(symbols_2, symbol_unit_len=4).add_space(unit=4, space=1) 249 | echo qua_2_hist 250 | 251 | 252 | var i: int = 0 253 | var f: File = open("example/example.fq") 254 | for rec in read_fastq(f): 255 | if i == 0: 256 | echo rec.to_string(hist_symbols=config.fq_config.hist.symbols) 257 | if i == 1: 258 | echo rec.to_string(hist_symbols=config.fq_config.hist.symbols, base_color=config.base_color) 259 | if i == 2: 260 | echo rec.to_string(hist_symbols=symbols_2, hist_symbol_unit_len=4, align=2) 261 | inc i 262 | f.close() 263 | 264 | let name1 = "@ST-E00126:415:HKVGNALXX:1:1101:2777:1836 1:N:0:GGACTC" 265 | let id1 = name1.parse_identifier() 266 | doAssert id1 != nil 267 | var parts_colors = config.fq_config.identifier.parts_colors 268 | parts_colors.instrument = Color(fg:10, bg:(-1)) 269 | parts_colors.index_seq = Color(fg:(-1), bg:20) 270 | echo id1.to_string(parts_colors) -------------------------------------------------------------------------------- /src/main.nim: -------------------------------------------------------------------------------- 1 | let doc = """ 2 | Command line tool for bioinformatics file format readability enhancement. 3 | 4 | Usage: 5 | bioview fq [--config-file=] [--hist=] [--color=] [--phred=<33/64>] [--delimiter=] 6 | bioview fa [--config-file=] [--color=] [--type=] 7 | bioview sam [--config-file=] [--hist=] [--color=] [--phred=<33/64>] [--multiline=] 8 | bioview color-atla 9 | bioview example-config 10 | bioview (-h | --help) 11 | 12 | Options: 13 | -h --help Show this help information. 14 | --phred=<33/64> Quality score encode for fastq file, 33 or 64. [33] 15 | --hist= Show quality hist or not. [yes] 16 | --delimiter= Show fastq record delimiter or not. [yes] 17 | --multiline= Show multiple line format of sam file. [no] 18 | --color= Show color height light of bases or not. [yes] 19 | --type= The record type of fasta file. [dna] 20 | --config-file= The path to config file. [~/.config/bioview/config.json] 21 | """ 22 | 23 | import os 24 | import tables 25 | 26 | import argparse 27 | 28 | import color_atla 29 | import fastq_utils 30 | import fasta_utils 31 | import sam_utils 32 | import configs 33 | 34 | var args = parse_args(doc) 35 | 36 | if args["color-atla"]: 37 | print_color_atla() 38 | quit(0) 39 | 40 | if args["example-config"]: 41 | example_json() 42 | quit(0) 43 | 44 | # write arguments to stderr, for debug 45 | when not defined(release): 46 | stderr.writeLine("arguments:") 47 | stderr.write($args & "\n") 48 | stderr.flushFile() 49 | 50 | # parse config 51 | let DEFAULT_CONFIG_PATH = getHomeDir().joinPath("/.config/bioview/config.json") 52 | var config: Config 53 | if args["--config-file"]: 54 | let conf = $args["--config-file"] 55 | if not existsFile(conf): 56 | stderr.writeLine("Config file " & conf & " not exist, use default config.") 57 | config = load_config(conf) 58 | else: 59 | if not existsFile(DEFAULT_CONFIG_PATH): 60 | stderr.writeLine("Warning: " & DEFAULT_CONFIG_PATH & " not exist.") 61 | config = load_config(DEFAULT_CONFIG_PATH) 62 | 63 | 64 | if (args["fq"]): 65 | # process fastq file 66 | 67 | case $args["--phred"] 68 | of "33": 69 | config.fq_config.phred = 33 70 | of "64": 71 | config.fq_config.phred = 64 72 | 73 | case $args["--hist"]: 74 | of "no": 75 | config.fq_config.hist.use = false 76 | of "yes": 77 | config.fq_config.hist.use = true 78 | 79 | case $args["--color"]: 80 | of "no": 81 | config.fq_config.use_color = false 82 | of "yes": 83 | config.fq_config.use_color = true 84 | 85 | case $args["--delimiter"]: 86 | of "no": 87 | config.fq_config.delimiter.use = false 88 | of "yes": 89 | config.fq_config.delimiter.use = true 90 | 91 | process_fastq($args[""], config) 92 | 93 | elif (args["fa"]): 94 | # process fasta file 95 | 96 | case $args["--color"]: 97 | of "no": 98 | config.fa_config.use_color = false 99 | of "yes": 100 | config.fa_config.use_color = true 101 | 102 | case $args["--type"]: 103 | of "dna": 104 | config.fa_config.record_type = "dna" 105 | of "rna": 106 | config.fa_config.record_type = "rna" 107 | of "protein": 108 | config.fa_config.record_type = "protein" 109 | 110 | process_fasta($args[""], config) 111 | 112 | elif (args["sam"]): 113 | # process sam file 114 | 115 | case $args["--phred"] 116 | of "33": 117 | config.fq_config.phred = 33 118 | of "64": 119 | config.fq_config.phred = 64 120 | 121 | case $args["--color"]: 122 | of "no": 123 | config.sam_config.use_color = false 124 | of "yes": 125 | config.sam_config.use_color = true 126 | 127 | case $args["--hist"]: 128 | of "no": 129 | config.sam_config.hist.use = false 130 | of "yes": 131 | config.sam_config.hist.use = true 132 | 133 | case $args["--multiline"]: 134 | of "no": 135 | config.sam_config.multiline = false 136 | of "yes": 137 | config.sam_config.multiline = true 138 | config.sam_config.delimiter.use = true 139 | 140 | case $args["--delimiter"]: 141 | of "no": 142 | config.sam_config.delimiter.use = false 143 | of "yes": 144 | config.sam_config.delimiter.use = true 145 | 146 | process_sam($args[""], config) -------------------------------------------------------------------------------- /src/sam_utils.nim: -------------------------------------------------------------------------------- 1 | import future 2 | import strutils 3 | 4 | from configs import Config, SamConfig, Delimiter 5 | from color_atla import colorize, colorize_seq, colorize_score, Color, ColorRange, BaseColor 6 | from fastq_utils import parse_quality, to_hist, encode_quality, add_space, to_string 7 | 8 | 9 | type 10 | 11 | OptionalField = tuple[tag:string, field_type:string, value:string] 12 | 13 | SamRecord = object 14 | qname: string 15 | flag: int 16 | rname: string 17 | pos: int 18 | mapq: int 19 | cigar: string 20 | rnext: string 21 | pnext: int 22 | tlen: int 23 | sequence: string 24 | qual: string 25 | optional_fields: seq[OptionalField] 26 | 27 | HeaderItem = tuple[name:string, value:string] 28 | 29 | SamHeader = object 30 | header_type: string 31 | items: seq[HeaderItem] 32 | 33 | 34 | proc parse_header(line:string): SamHeader = 35 | let items = line.split("\t") 36 | let header_type = items[0][1.. 1: 125 | seq_str = seq_str.add_space(unit=1, space=(config.hist.align - 1)) 126 | hist_str = hist_str.add_space(unit=config.hist.symbol_unit_len, space=(config.hist.align - 1)) 127 | 128 | let ofc = config.optional_fields_color 129 | 130 | if config.use_color: 131 | qname_str = qname_str.colorize(config.qname_color) 132 | flag_str = flag_str.colorize(config.flag_color) 133 | rname_str = rname_str.colorize(config.rname_color) 134 | pos_str = pos_str.colorize(config.pos_color) 135 | mapq_str = mapq.colorize_score(config.mapq_color_range) 136 | cigar_str = cigar_str.colorize(config.cigar_color) 137 | rnext_str = rnext_str.colorize(config.rnext_color) 138 | pnext_str = pnext_str.colorize(config.pnext_color) 139 | tlen_str = tlen_str.colorize(config.tlen_color) 140 | if config.use_base_color: 141 | seq_str = seq_str.colorize_seq(base_color) 142 | hist_str = hist_str.colorize(config.hist.color) 143 | 144 | let optional_items = 145 | lc[ ( item.tag.colorize(ofc.tag) & ":" & item.field_type.colorize(ofc.field_type) & ":" & item.value.colorize(ofc.value) ) | (item <- rec.optional_fields), string ] 146 | optional_str = optional_items.join("\t") 147 | else: 148 | mapq_str = mapq.intToStr 149 | 150 | let optional_items = 151 | lc[ ( item.tag & ":" & item.field_type & ":" & item.value ) | (item <- rec.optional_fields), string ] 152 | optional_str = optional_items.join("\t") 153 | 154 | if not config.multiline: 155 | result = 156 | qname_str & "\t" & flag_str & "\t" & rname_str & "\t" & 157 | pos_str & "\t" & mapq_str & "\t" & cigar_str & "\t" & 158 | rnext_str & "\t" & pnext_str & "\t" & tlen_str & "\t" & 159 | seq_str & "\t" & hist_str & "\t" & optional_str 160 | else: 161 | result = 162 | "query_name: " & qname_str & "\t" & "flag: " & flag_str & "\t" & "ref_name: " & rname_str & "\n" & 163 | "position: " & pos_str & "\t" & "mapq: " & mapq_str & "\t" & "cigar: " & cigar_str & "\n" & 164 | "next: " & rnext_str & "\t" & pnext_str & "\t" & "templete_len: " & tlen_str & "\n" & 165 | seq_str & "\n" & hist_str & "\n" & 166 | optional_str 167 | 168 | 169 | proc process_sam*(fname:string, config:Config) = 170 | var f: File 171 | if fname == "-": 172 | f = stdin 173 | else: 174 | if open(f, fname): 175 | discard 176 | else: 177 | raise newException(IOError, fname & " can not open.") 178 | 179 | for line in f.lines: 180 | 181 | if line.startswith("@"): 182 | let header = parse_header(line) 183 | let hc = config.sam_config.header_color 184 | echo header.to_string(hc.header_type, hc.item_key, hc.item_value, config.sam_config.use_color) 185 | else: 186 | if config.sam_config.delimiter.use: 187 | echo config.sam_config.delimiter.to_string() 188 | let rec = parse_record(line) 189 | echo rec.to_string(config.base_color, config.sam_config) 190 | 191 | if config.sam_config.delimiter.use: 192 | echo config.sam_config.delimiter.to_string() 193 | 194 | 195 | when isMainModule: 196 | import configs 197 | let config = load_config() 198 | let sam_conf = config.sam_config 199 | 200 | let header_line_1 = "@SQ SN:chr1 LN:248956422" 201 | let header_line_2 = "@PG ID:bwa PN:bwa VN:0.7.15-r1140 CL:bwa samse ./data/BWA_index/genome.fa test_left.bwa hookers_test_left.fq" 202 | 203 | var 204 | hc = sam_conf.header_color.header_type 205 | kc = sam_conf.header_color.item_key 206 | vc = sam_conf.header_color.item_value 207 | 208 | let header_1 = parse_header(header_line_1) 209 | echo header_1.to_string(hc, kc, vc, true) 210 | 211 | let header_2 = parse_header(header_line_2) 212 | echo header_2.to_string(hc, kc, vc, true) -------------------------------------------------------------------------------- /test.sh: -------------------------------------------------------------------------------- 1 | #!/bin/bash -e 2 | 3 | # usage: 4 | # ./test.sh 5 | # ./test.sh 6 | # 7 | # e.g. 8 | # ./test.sh configs # test configs.nim moudle 9 | # ./test.sh # test all moudles 10 | 11 | function test { 12 | moudle=$1 13 | moudle_path=src/$moudle.nim 14 | 15 | echo "=============================" 16 | echo test $moudle_path 17 | echo "=============================" 18 | 19 | nim c -r $moudle_path 20 | exe="src/$moudle" 21 | rm $exe 22 | } 23 | 24 | function test_all { 25 | for nimf in `ls src`; 26 | do 27 | if [ $nimf == 'main.nim' ] || [ -d src/$nimf ] ; then 28 | continue 29 | fi 30 | 31 | moudle=$(echo $nimf | sed 's/.nim$//') 32 | 33 | test $moudle 34 | 35 | done 36 | } 37 | 38 | if [ $# -eq 0 ]; then 39 | test_all 40 | else 41 | moudle=$1 42 | test $moudle 43 | fi 44 | -------------------------------------------------------------------------------- /theme/README.md: -------------------------------------------------------------------------------- 1 | # Themes 2 | 3 | ## Simple (default) 4 | 5 | Use the following command switch to this theme. 6 | 7 | ```bash 8 | $ mkdir -p ~/.config/bioview/ ; curl -LJ https://raw.githubusercontent.com/Nanguage/bioView/master/theme/simple.json -o ~/.config/bioview/config.json 9 | ``` 10 | 11 | ### glimpse 12 | 13 | #### Fastq 14 | 15 | ![simple-fq](../example/imgs/theme_glimpse/simple/simple-fq.png) 16 | 17 | #### Fasta 18 | 19 | ![simple-fa](../example/imgs/theme_glimpse/simple/simple-fa.png) 20 | 21 | #### Sam 22 | 23 | ![simple-sam](../example/imgs/theme_glimpse/simple/simple-sam.png) 24 | 25 | ## Verbose 26 | 27 | ```bash 28 | $ mkdir -p ~/.config/bioview/ ; curl -LJ https://raw.githubusercontent.com/Nanguage/bioView/master/theme/verbose.json n -o ~/.config/bioview/config.json 29 | ``` 30 | 31 | ### glimpse 32 | 33 | #### Fastq 34 | 35 | ![verbose-fq](../example/imgs/theme_glimpse/verbose/verbose-fq.png) 36 | 37 | #### Fasta 38 | 39 | Same to Simple. 40 | 41 | #### Sam 42 | 43 | ![verbose-sam](../example/imgs/theme_glimpse/verbose/verbose-sam.png) 44 | 45 | ## Emoji 46 | 47 | ```bash 48 | $ mkdir -p ~/.config/bioview/ ; curl -LJ https://raw.githubusercontent.com/Nanguage/bioView/master/theme/emoji.json -o ~/.config/bioview/config.json 49 | ``` 50 | 51 | ### glimpse 52 | 53 | #### Fastq 54 | 55 | ![emoji-fq](../example/imgs/theme_glimpse/emoji/emoji-fq.png) 56 | 57 | #### Fasta 58 | 59 | Same to Simple. 60 | 61 | #### Sam 62 | 63 | ![emoji-sam](../example/imgs/theme_glimpse/emoji/emoji-sam.png) 64 | -------------------------------------------------------------------------------- /theme/emoji.json: -------------------------------------------------------------------------------- 1 | { 2 | "base_color": 3 | { 4 | "A": {"fg": 196, "bg": -1}, 5 | "T": {"fg": 50 , "bg": -1}, 6 | "C": {"fg": 226, "bg": -1}, 7 | "G": {"fg": 82 , "bg": -1}, 8 | "U": {"fg": -1, "bg": -1}, 9 | "N": {"fg": -1, "bg": -1} 10 | }, 11 | 12 | "fq_config": 13 | { 14 | "phred": 33, 15 | 16 | "use_color": true, 17 | "use_base_color": true, 18 | 19 | "hist": { 20 | "use": true, 21 | "symbols": 22 | "👿👿👿👿👿😫😫😫😫😫🙁🙁🙁🙁🙁😣😣😣😣😣🙃🙃🙃🙃🙃😑😑😑😑😑🙂🙂🙂🙂🙂😃😃😃😃😃", 23 | "symbol_unit_len": 4, 24 | "align": 2, 25 | "color": {"fg": -1, "bg": -1} 26 | }, 27 | 28 | "identifier": { 29 | "color": {"fg": -1, "bg": -1}, 30 | "parse_parts": false, 31 | "parts_colors": { 32 | "instrument": {"fg": -1, "bg": -1}, 33 | "run_id": {"fg": -1, "bg": -1}, 34 | "flowcell_id": {"fg": -1, "bg": -1}, 35 | "tile_number": {"fg": -1, "bg": -1}, 36 | "x_coordinate": {"fg": -1, "bg": -1}, 37 | "y_coordinate": {"fg": -1, "bg": -1}, 38 | "pair": {"fg": -1, "bg": -1}, 39 | "filtered": {"fg": -1, "bg": -1}, 40 | "control_bits": {"fg": -1, "bg": -1}, 41 | "index_seq": {"fg": -1, "bg": -1} 42 | } 43 | }, 44 | 45 | "delimiter": { 46 | "use": true, 47 | "str": "-", 48 | "len": 150, 49 | "color": {"fg": -1, "bg": -1} 50 | } 51 | 52 | }, 53 | 54 | "fa_config": 55 | { 56 | "use_color": true, 57 | "use_base_color": true, 58 | 59 | "record_type": "dna", 60 | 61 | "amino_color": { 62 | "A": {"fg": 1, "bg": -1}, 63 | "R": {"fg": 2, "bg": -1}, 64 | "N": {"fg": 3, "bg": -1}, 65 | "D": {"fg": 4, "bg": -1}, 66 | "C": {"fg": 5, "bg": -1}, 67 | "E": {"fg": 6, "bg": -1}, 68 | "Q": {"fg": 7, "bg": -1}, 69 | "G": {"fg": 8, "bg": -1}, 70 | "H": {"fg": 9, "bg": -1}, 71 | "I": {"fg": 10, "bg": -1}, 72 | "L": {"fg": 11, "bg": -1}, 73 | "K": {"fg": 12, "bg": -1}, 74 | "M": {"fg": 13, "bg": -1}, 75 | "F": {"fg": 14, "bg": -1}, 76 | "P": {"fg": 15, "bg": -1}, 77 | "S": {"fg": 16, "bg": -1}, 78 | "T": {"fg": 17, "bg": -1}, 79 | "W": {"fg": 18, "bg": -1}, 80 | "Y": {"fg": 19, "bg": -1}, 81 | "V": {"fg": 20, "bg": -1} 82 | }, 83 | 84 | "identifier_color": {"fg": -1, "bg": -1} 85 | }, 86 | 87 | "sam_config": 88 | { 89 | "phred": 33, 90 | 91 | "use_color": true, 92 | 93 | "multiline": true, 94 | 95 | "delimiter": { 96 | "use": true, 97 | "str": "-", 98 | "len": 150, 99 | "color": {"fg": -1, "bg": -1} 100 | }, 101 | 102 | "header_color": { 103 | "header_type": {"fg": 111, "bg": -1}, 104 | "item_key": {"fg": 201, "bg": -1}, 105 | "item_value": {"fg": 202, "bg": -1} 106 | }, 107 | 108 | "qname_color": {"fg": 40, "bg": -1}, 109 | "flag_color": {"fg": 196, "bg": -1}, 110 | "rname_color": {"fg": 184, "bg": -1}, 111 | "pos_color": {"fg": 122, "bg": -1}, 112 | 113 | "mapq_color_range": { 114 | "buttom": {"val": 0, "color": {"fg": -1, "bg": 232}}, 115 | "top": {"val": 30, "color": {"fg": -1, "bg": 255}} 116 | }, 117 | 118 | "cigar_color": {"fg": 225, "bg": -1}, 119 | "rnext_color": {"fg": 63, "bg": -1}, 120 | "pnext_color": {"fg": 64, "bg": -1}, 121 | "tlen_color": {"fg": 200, "bg": -1}, 122 | 123 | "optional_fields_color": { 124 | "tag": {"fg": 14, "bg": -1}, 125 | "field_type": {"fg": 134, "bg": -1}, 126 | "value": {"fg": 210, "bg": -1} 127 | }, 128 | 129 | "use_base_color": true, 130 | 131 | "hist": { 132 | "use": true, 133 | "symbols": 134 | "👿👿👿👿👿😫😫😫😫😫🙁🙁🙁🙁🙁😣😣😣😣😣🙃🙃🙃🙃🙃😑😑😑😑😑🙂🙂🙂🙂🙂😃😃😃😃😃", 135 | "symbol_unit_len": 4, 136 | "align": 2, 137 | "color": {"fg": -1, "bg": -1} 138 | } 139 | } 140 | } -------------------------------------------------------------------------------- /theme/simple.json: -------------------------------------------------------------------------------- 1 | { 2 | "base_color": 3 | { 4 | "A": {"fg": 196, "bg": -1}, 5 | "T": {"fg": 50 , "bg": -1}, 6 | "C": {"fg": 226, "bg": -1}, 7 | "G": {"fg": 82 , "bg": -1}, 8 | "U": {"fg": -1, "bg": -1}, 9 | "N": {"fg": -1, "bg": -1} 10 | }, 11 | 12 | "fq_config": 13 | { 14 | "phred": 33, 15 | 16 | "use_color": true, 17 | "use_base_color": true, 18 | 19 | "hist": { 20 | "use": true, 21 | "symbols": 22 | "▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████", 23 | "symbol_unit_len": 3, 24 | "align": 1, 25 | "color": {"fg": -1, "bg": -1} 26 | }, 27 | 28 | "identifier": { 29 | "color": {"fg": -1, "bg": -1}, 30 | "parse_parts": false, 31 | "parts_colors": { 32 | "instrument": {"fg": -1, "bg": -1}, 33 | "run_id": {"fg": -1, "bg": -1}, 34 | "flowcell_id": {"fg": -1, "bg": -1}, 35 | "tile_number": {"fg": -1, "bg": -1}, 36 | "x_coordinate": {"fg": -1, "bg": -1}, 37 | "y_coordinate": {"fg": -1, "bg": -1}, 38 | "pair": {"fg": -1, "bg": -1}, 39 | "filtered": {"fg": -1, "bg": -1}, 40 | "control_bits": {"fg": -1, "bg": -1}, 41 | "index_seq": {"fg": -1, "bg": -1} 42 | } 43 | }, 44 | 45 | "delimiter": { 46 | "use": true, 47 | "str": "-", 48 | "len": 150, 49 | "color": {"fg": -1, "bg": -1} 50 | } 51 | 52 | }, 53 | 54 | "fa_config": 55 | { 56 | "use_color": true, 57 | "use_base_color": true, 58 | 59 | "record_type": "dna", 60 | 61 | "amino_color": { 62 | "A": {"fg": 1, "bg": -1}, 63 | "R": {"fg": 2, "bg": -1}, 64 | "N": {"fg": 3, "bg": -1}, 65 | "D": {"fg": 4, "bg": -1}, 66 | "C": {"fg": 5, "bg": -1}, 67 | "E": {"fg": 6, "bg": -1}, 68 | "Q": {"fg": 7, "bg": -1}, 69 | "G": {"fg": 8, "bg": -1}, 70 | "H": {"fg": 9, "bg": -1}, 71 | "I": {"fg": 10, "bg": -1}, 72 | "L": {"fg": 11, "bg": -1}, 73 | "K": {"fg": 12, "bg": -1}, 74 | "M": {"fg": 13, "bg": -1}, 75 | "F": {"fg": 14, "bg": -1}, 76 | "P": {"fg": 15, "bg": -1}, 77 | "S": {"fg": 16, "bg": -1}, 78 | "T": {"fg": 17, "bg": -1}, 79 | "W": {"fg": 18, "bg": -1}, 80 | "Y": {"fg": 19, "bg": -1}, 81 | "V": {"fg": 20, "bg": -1} 82 | }, 83 | 84 | "identifier_color": {"fg": -1, "bg": -1} 85 | }, 86 | 87 | "sam_config": 88 | { 89 | "phred": 33, 90 | 91 | "use_color": true, 92 | 93 | "multiline": false, 94 | 95 | "delimiter": { 96 | "use": false, 97 | "str": "-", 98 | "len": 150, 99 | "color": {"fg": -1, "bg": -1} 100 | }, 101 | 102 | "header_color": { 103 | "header_type": {"fg": 111, "bg": -1}, 104 | "item_key": {"fg": 201, "bg": -1}, 105 | "item_value": {"fg": 202, "bg": -1} 106 | }, 107 | 108 | "qname_color": {"fg": 40, "bg": -1}, 109 | "flag_color": {"fg": 196, "bg": -1}, 110 | "rname_color": {"fg": 184, "bg": -1}, 111 | "pos_color": {"fg": 122, "bg": -1}, 112 | 113 | "mapq_color_range": { 114 | "buttom": {"val": 0, "color": {"fg": -1, "bg": 232}}, 115 | "top": {"val": 30, "color": {"fg": -1, "bg": 255}} 116 | }, 117 | 118 | "cigar_color": {"fg": 225, "bg": -1}, 119 | "rnext_color": {"fg": 63, "bg": -1}, 120 | "pnext_color": {"fg": 64, "bg": -1}, 121 | "tlen_color": {"fg": 200, "bg": -1}, 122 | 123 | "optional_fields_color": { 124 | "tag": {"fg": 14, "bg": -1}, 125 | "field_type": {"fg": 134, "bg": -1}, 126 | "value": {"fg": 210, "bg": -1} 127 | }, 128 | 129 | "use_base_color": true, 130 | 131 | "hist": { 132 | "use": true, 133 | "symbols": 134 | "▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████", 135 | "symbol_unit_len": 3, 136 | "align": 1, 137 | "color": {"fg": -1, "bg": -1} 138 | } 139 | 140 | } 141 | } 142 | 143 | -------------------------------------------------------------------------------- /theme/verbose.json: -------------------------------------------------------------------------------- 1 | { 2 | "base_color": 3 | { 4 | "A": {"fg": 196, "bg": -1}, 5 | "T": {"fg": 50 , "bg": -1}, 6 | "C": {"fg": 226, "bg": -1}, 7 | "G": {"fg": 82 , "bg": -1}, 8 | "U": {"fg": -1, "bg": -1}, 9 | "N": {"fg": -1, "bg": -1} 10 | }, 11 | 12 | "fq_config": 13 | { 14 | "phred": 33, 15 | 16 | "use_color": true, 17 | "use_base_color": true, 18 | 19 | "hist": { 20 | "use": true, 21 | "symbols": 22 | "▁▁▁▁▁▁▁▁▂▂▂▂▂▃▃▃▃▃▄▄▄▄▄▅▅▅▅▅▆▆▆▆▆▇▇▇▇▇██████", 23 | "symbol_unit_len": 3, 24 | "align": 1, 25 | "color": {"fg": -1, "bg": -1} 26 | }, 27 | 28 | "identifier": { 29 | "color": {"fg": -1, "bg": -1}, 30 | "parse_parts": true, 31 | "parts_colors": { 32 | "instrument": {"fg": -1, "bg": 210}, 33 | "run_id": {"fg": -1, "bg": 90}, 34 | "flowcell_id": {"fg": -1, "bg": 100}, 35 | "tile_number": {"fg": -1, "bg": 83}, 36 | "x_coordinate": {"fg": -1, "bg": 1}, 37 | "y_coordinate": {"fg": -1, "bg": 2}, 38 | "pair": {"fg": -1, "bg": 160}, 39 | "filtered": {"fg": -1, "bg": 124}, 40 | "control_bits": {"fg": -1, "bg": 87}, 41 | "index_seq": {"fg": 81, "bg": -1} 42 | } 43 | }, 44 | 45 | "delimiter": { 46 | "use": true, 47 | "str": "-", 48 | "len": 150, 49 | "color": {"fg": -1, "bg": -1} 50 | } 51 | 52 | }, 53 | 54 | "fa_config": 55 | { 56 | "use_color": true, 57 | "use_base_color": true, 58 | 59 | "record_type": "dna", 60 | 61 | "amino_color": { 62 | "A": {"fg": 1, "bg": -1}, 63 | "R": {"fg": 2, "bg": -1}, 64 | "N": {"fg": 3, "bg": -1}, 65 | "D": {"fg": 4, "bg": -1}, 66 | "C": {"fg": 5, "bg": -1}, 67 | "E": {"fg": 6, "bg": -1}, 68 | "Q": {"fg": 7, "bg": -1}, 69 | "G": {"fg": 8, "bg": -1}, 70 | "H": {"fg": 9, "bg": -1}, 71 | "I": {"fg": 10, "bg": -1}, 72 | "L": {"fg": 11, "bg": -1}, 73 | "K": {"fg": 12, "bg": -1}, 74 | "M": {"fg": 13, "bg": -1}, 75 | "F": {"fg": 14, "bg": -1}, 76 | "P": {"fg": 15, "bg": -1}, 77 | "S": {"fg": 16, "bg": -1}, 78 | "T": {"fg": 17, "bg": -1}, 79 | "W": {"fg": 18, "bg": -1}, 80 | "Y": {"fg": 19, "bg": -1}, 81 | "V": {"fg": 20, "bg": -1} 82 | }, 83 | 84 | "identifier_color": {"fg": -1, "bg": -1} 85 | }, 86 | 87 | "sam_config": 88 | { 89 | "phred": 33, 90 | 91 | "use_color": 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