Commit ca116ec2 authored by Dylan Aïssi's avatar Dylan Aïssi

New upstream version 0.1~beta4+dfsg

parent 9f721623
# .gitattributes file
# Folders and files listed here are EXCLUDED from deployment
# when using `git archive` or github release
# Git Files
.gitattributes export-ignore
.gitignore export-ignore
# Development Folder
dev/* export-ignore
# Images
bioSyntax_logo.png export-ignore
# Extra licenses/readme in submodules
vim/README.md export-ignore
vim/LICENSE.md export-ignore
sublime/README.md export-ignore
sublime/LICENSE.md export-ignore
local/*
*.Rproj
*.Rproj.user
.Rhistory
.swp
*.swp
*.sublime-project
examples/vcf/test_1000genomes.vcf
// GENERIC SYNTAX
// bioSyntax Settings File
// These settings override both User and Default settings
// for this syntax
{
// Sets the colors used within the text area
"color_scheme": "Packages/bioSyntax/bioSyntax.tmTheme",
// Word Wrapping
"word_wrap": false,
// Line Number / Gutter -- User controlled
//"line_numbers": true,
//"gutter": true,
//"margin": 4,
}
%YAML 1.2
---
# Bed syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: bed
file_extensions: [bed]
scope: source.bed
contexts:
main:
#Handle UCSC track line
- match: '^track.*'
scope: comment.bed
# Column 1: Reference Sequence Name
- match: '^[\S]*\t'
scope: chr.bed
push: start
# Column 2: Start coordinate
start:
- match: ([0-9|\.](?=\d{2}\t))
scope: chrStart2.bed
- match: ([0-9|\.](?=\d{5}\t))
scope: chrStart2.bed
- match: ([0-9|\.](?=\d{8}\t))
scope: chrStart2.bed
- match: ([0-9|\.])
scope: chrStart.bed
- match: \t
push: end
- match: $
pop: true
# Column 3: End Coordinate
end:
- match: ([0-9|\.](?=\d{2}\t))
scope: chrStart2.bed
- match: ([0-9|\.](?=\d{5}\t))
scope: chrStart2.bed
- match: ([0-9|\.](?=\d{8}\t))
scope: chrStart2.bed
- match: ([0-9|\.])
scope: chrStart.bed
- match: \t
push: name
- match: $
pop: true
# Column 4: Description / Name
name:
- match: '[\S]*'
scope: string.bed
- match: \t
push: score
- match: $
pop: true
# Column 5: Score (0-1000 scale)
score:
- match: \.\b
scope: comment.bed
- match: ([0-9])\b
scope: grad1.bed
- match: ([1-9][0-9])\b
scope: grad1.bed
- match: 1[0-9][0-9]\b
scope: grad2.bed
- match: 2[0-9][0-9]\b
scope: grad3.bed
- match: 3[0-9][0-9]\b
scope: grad4.bed
- match: 4[0-9][0-9]\b
scope: grad5.bed
- match: 5[0-9][0-9]\b
scope: grad6.bed
- match: 6[0-9][0-9]\b
scope: grad7.bed
- match: 7[0-9][0-9]\b
scope: grad8.bed
- match: 8[0-9][0-9]\b
scope: grad9.bed
- match: 9[0-9][0-9]\b
scope: grad10.bed
- match: ([0-9][0-9][0-9][0-9])\b
scope: grad10.bed
- match: \t
push: strand
- match: $
pop: true
# Column 6: Feature Strand
strand:
- match: \+
scope: strandPlus.bed
- match: \-
scope: strandMinus.bed
- match: \.
scope: strandNone.bed
- match: $
pop: true
\ No newline at end of file
// GENERIC SYNTAX
// bioSyntax Settings File
// These settings override both User and Default settings
// for this syntax
{
// Sets the colors used within the text area
"color_scheme": "Packages/bioSyntax/bioSyntax.tmTheme",
// Word Wrapping
"word_wrap": false,
// Line Number / Gutter -- User controlled
//"line_numbers": true,
//"gutter": true,
//"margin": 4,
}
This diff is collapsed.
// GENERIC SYNTAX
// bioSyntax Settings File
// These settings override both User and Default settings
// for this syntax
{
// Sets the colors used within the text area
"color_scheme": "Packages/bioSyntax/bioSyntax.tmTheme",
// Word Wrapping
"word_wrap": false,
// Line Number / Gutter -- User controlled
//"line_numbers": true,
//"gutter": true,
//"margin": 4,
}
%YAML 1.2
---
# Clustal syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: clustal
# See http://www.sublimetext.com/docs/3/syntax.html
file_extensions: [clustal,aln]
scope: text.clustal
contexts:
main:
# Main Identifier
- match: "^CLUSTAL.*"
scope: comment
# Sequence Identifier
- match: "/[0-9]*-[0-9]*" #Optional sequence range
scope: chrStart
- match: "^[\\w\\.\\-\\_]*(?=[/ ])" #Spaces not allowed in seqname
scope: string
# Optional trailing numeric
- match: "[0-9]+$"
scope: chrStart
# Optional: Conservation
- match: "\\*++"
scope: null
- match: "\\:++"
scope: gradbw5
- match: "\\.++"
scope: gradbw5
# match Adenosine
- match: "[Aa]++"
scope: ntA
# match Cytidine
- match: "[Cc]++"
scope: ntC
# match Guanine
- match: "[Gg]++"
scope: ntG
# match Thymidine/Uridine
- match: "[TtUu]++"
scope: ntT
# aNy or unknown (X)
- match: "[NnXx]++"
scope: ntN
# indel
- match: "[-]++"
scope: ntGap
# Match Extended Nucleotides
- match: "[Rr]++"
scope: ntR
- match: "[Yy]++"
scope: ntY
- match: "[Ss]++"
scope: ntS
- match: "[Ww]++"
scope: ntW
- match: "[Mm]++"
scope: ntM
- match: "[Kk]++"
scope: ntK
- match: "[Dd]++"
scope: ntD
- match: "[Bb]++"
scope: ntB
- match: "[Vv]++"
scope: ntV
- match: "[Hh]++"
scope: ntH
// GENERIC SYNTAX
// bioSyntax Settings File
// These settings override both User and Default settings
// for this syntax
{
// Sets the colors used within the text area
"color_scheme": "Packages/bioSyntax/bioSyntax.tmTheme",
// Word Wrapping
"word_wrap": "auto",
// Line Number / Gutter -- User controlled
//"line_numbers": true,
//"gutter": true,
//"margin": 4,
}
%YAML 1.2
---
# CWL syntax highlighting file
# Maintainer: Manabu Ishii
# Source: https://github.com/manabuishii
name: CWL
# See http://www.sublimetext.com/docs/3/syntax.html
file_extensions:
- cwl
scope: source.cwl
contexts:
# The prototype context is prepended to all contexts but those setting
# meta_include_prototype: false.
prototype:
- include: comments
main:
# The main context is the initial starting point of our syntax.
# Include other contexts from here (or specify them directly).
- include: keywords
- include: type
- include: constant
- include: double_quoted_strings
- include: single_quoted_strings
keywords:
- match: '\b(class|cwlVersion|dockerPull|inputs|outputs|steps|id|requirements|hints|label|doc|secondaryFiles|streamable|outputBinding|format|outputSource|linkMerge|type|glob|loadContents|outputEval|merge_nested|merge_flattened|location|path|basename|dirname|nameroot|nameext|checksum|size|format|contents|listing|fields|symbols|items|in|out|run|scatter|scatterMethod|source|default|valueFrom|expressionLib|types|linkMerge|inputBinding|position|prefix|separate|itemSeparator|valueFrom|shellQuote|packages|package|version|specs|entry|entryname|writable|baseCommand|arguments|stdin|stderr|stdout|successCodes|temporaryFailCodes|permanentFailCodes|dockerLoad|dockerFile|dockerImport|dockerImageId|dockerOutputDirectory|envDef|envName|envValue|coresMin|coresMax|ramMin|ramMax|tmpdirMin|tmpdirMax|outdirMin|outdirMax)(?=:)'
scope: keyword.control.cwl
type:
- match: '\b(CommandLineTool|ExpressionTool|Workflow|InlineJavascriptRequirement|SchemaDefRequirement|DockerRequirement|SoftwareRequirement|InitialWorkDirRequirement|EnvVarRequirement|ShellCommandRequirement|ResourceRequirement)\b'
scope: support.type.cwl
constant:
- match: ':\s+(null|boolean|int|long|float|double|string|File|Directory)\b'
scope: storage.type.cwl
# double quoted string
double_quoted_strings:
- match: '"'
scope: punctuation.definition.string.begin.cwl
push: inside_double_quoted_string
inside_double_quoted_string:
- meta_include_prototype: false
- meta_scope: string.quoted.double.cwl
- match: '\.'
scope: constant.character.escape.cwl
- match: '"'
scope: punctuation.definition.string.end.cwl
pop: true
# single quoted string
single_quoted_strings:
- match: \'
scope: punctuation.definition.string.begin.cwl
push: inside_single_quoted_string
inside_single_quoted_string:
- meta_include_prototype: false
- meta_scope: string.quoted.single.cwl
- match: '\.'
scope: constant.character.escape.cwl
- match: \'
scope: punctuation.definition.string.end.cwl
pop: true
comments:
# Comments begin with a '#' and finish at the end of the line.
- match: '#.*$'
scope: punctuation.definition.comment.cwl
push:
# This is an anonymous context push for brevity.
- meta_scope: comment.line.number-sign.cwl
- match: $\n?
pop: true
# MIT License
# Copyright (c) 2018 Manabu ISHII
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
# The above copyright notice and this permission notice shall be included in all
# copies or substantial portions of the Software.
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
# SOFTWARE.
\ No newline at end of file
// GENERIC SYNTAX
// bioSyntax Settings File
// These settings override both User and Default settings
// for this syntax
{
// Sets the colors used within the text area
"color_scheme": "Packages/bioSyntax/bioSyntax.tmTheme",
// Word Wrapping
"word_wrap": false,
// Line Number / Gutter -- User controlled
//"line_numbers": true,
//"gutter": true,
//"margin": 4,
}
%YAML 1.2
---
# Fasta Index (faidx) syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: faidx
# See http://www.sublimetext.com/docs/3/syntax.html
file_extensions: [fai,fai]
scope: source.faidx
# Fasta Index Filetype Description
# NAME Name of this reference sequence
# LENGTH Total length of this reference sequence, in bases
# OFFSET Offset within the FASTA file of this sequence's first base
# LINEBASES The number of bases on each line
# LINEWIDTH The number of bytes in each line, including the newline
contexts:
main:
# COLUMN 1
- match: '^[\S]*\t'
scope: chr.faidx
push: contig.length
# COLUMN 3
- match: '(?<=\t)[\S]*\t'
scope: numeric.faidx
push: genomic.offset
# COLUMN 5
- match: '[\S]*$'
scope: comment.faidx
contig.length:
# COLUMN 2
- match: '[\S]*'
scope: chrStart.faidx
- match: \t
pop: true
genomic.offset:
# COLUMN 4
- match: '[\S]*'
scope: comment.faidx
- match: \t
pop: true
\ No newline at end of file
// GENERIC SYNTAX
// bioSyntax Settings File
// These settings override both User and Default settings
// for this syntax
{
// Sets the colors used within the text area
"color_scheme": "Packages/bioSyntax/bioSyntax.tmTheme",
// Word Wrapping
"word_wrap": false,
// Line Number / Gutter -- User controlled
//"line_numbers": true,
//"gutter": true,
//"margin": 4,
}
%YAML 1.2
---
# Fasta-Clustal syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: fasta-clustal
# See http://www.sublimetext.com/docs/3/syntax.html
file_extensions: [fastaa,faa]
scope: text.fasta-clustal
contexts:
main:
#positive lookbehind to match a + and a new line to any characters right after it
#pushes it to quality
- match: "^>.*"
scope: string
# match amino acids
# Alanine (ALA)
- match: "[Aa]++"
scope: aaA
# Aspartate/Asparagine (ASX)
- match: "[Bb]++"
scope: aaB
# Cysteine (CYS)
- match: "[Cc]++"
scope: aaC
# Aspartate (ASP)
- match: "[Dd]++"
scope: aaD
# Glutamate (GLU)
- match: "[Ee]++"
scope: aaE
# Phenylalanine (PHE)
- match: "[Ff]++"
scope: aaF
# Glycine (GLY)
- match: "[Gg]++"
scope: aaG
# Histidine (HIS)
- match: "[Hh]++"
scope: aaH
# Isoleucine (ILE)
- match: "[Ii]++"
scope: aaI
# Lysine (LYS)
- match: "[Kk]++"
scope: aaK
# Leucine (LEU)
- match: "[Ll]++"
scope: aaL
# Methionine (MET)
- match: "[Mm]++"
scope: aaM
# Asparagine (ASN)
- match: "[Nn]++"
scope: aaN
# Proline (PRO)
- match: "[Pp]++"
scope: aaP
# Glutamine (GLN)
- match: "[Qq]++"
scope: aaQ
# Arginine (ARG)
- match: "[Rr]++"
scope: aaR
# Serine (SER)
- match: "[Ss]++"
scope: aaS
# Threonine (THE)
- match: "[Tt]++"
scope: aaT
# Valine (VAL)
- match: "[Vv]++"
scope: aaV
# Tryptophan (TRP)
- match: "[Ww]++"
scope: aaW
# Tyrosine (TYR)
- match: "[Yy]++"
scope: aaY
# Glutamate or Glutamine (GLX)
- match: "[Zz]++"
scope: aaZ
# any/unknown (X)
- match: "[Xx]++"
scope: zappo.X
# translation stop
- match: "\\*"
scope: comment
# indel
- match: "[-]++"
scope: comment
// GENERIC SYNTAX
// bioSyntax Settings File
// These settings override both User and Default settings
// for this syntax
{
// Sets the colors used within the text area
"color_scheme": "Packages/bioSyntax/bioSyntax.tmTheme",
// Word Wrapping
"word_wrap": false,
// Line Number / Gutter -- User controlled
//"line_numbers": true,
//"gutter": true,
//"margin": 4,
}
%YAML 1.2
---
# Fasta-Nucleotides syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: fasta
# See http://www.sublimetext.com/docs/3/syntax.html
file_extensions: [.fasta,.fa,.fas,.mfa]
scope: text.fasta
contexts:
main:
# Fasta Header
- match: "^>.*"
scope: header
# Match Nucleotides
# match Adenosine
- match: "[Aa]++"
scope: ntA
# match Cytidine
- match: "[Cc]++"
scope: ntC
# match Guanine
- match: "[Gg]++"
scope: ntG
# match Thymidine
- match: "[Tt]++"
scope: ntT
# match Uridine
- match: "[Uu]++"
scope: ntU
# match aNy or unknown (X)
- match: "[NnXx]++"
scope: ntN
# indel
- match: "[-]"
scope: ntGap
# Match Extended Nucleotides
- match: "[Rr]++"
scope: ntR
- match: "[Yy]++"
scope: ntY
- match: "[Ss]++"
scope: ntS
- match: "[Ww]++"
scope: ntW
- match: "[Mm]++"
scope: ntM
- match: "[Kk]++"
scope: ntK
- match: "[Dd]++"
scope: ntD
- match: "[Bb]++"
scope: ntB
- match: "[Vv]++"
scope: ntV
- match: "[Hh]++"
scope: ntH
// GENERIC SYNTAX
// bioSyntax Settings File
// These settings override both User and Default settings
// for this syntax
{
// Sets the colors used within the text area
"color_scheme": "Packages/bioSyntax/bioSyntax.tmTheme",
// Word Wrapping
"word_wrap": false,
// Line Number / Gutter -- User controlled
//"line_numbers": true,
//"gutter": true,
//"margin": 4,
}
%YAML 1.2
---
# Fasta-Hydrophobicity syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: fasta-hydro
# See http://www.sublimetext.com/docs/3/syntax.html
file_extensions: [fastahydro]
scope: text.fasta-hydro
contexts:
main:
#positive lookbehind to match a + and a new line to any characters right after it
#pushes it to quality
- match: "^>.*"
scope: string
# match amino acids
# Alanine (ALA)