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ababaian
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Initialize Sublime syntax
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‎Color Scheme - bioSyntax.sublime-package

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‎bed.sublime-syntax

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%YAML 1.2
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---
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# Bed syntax highlighting file
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# Maintainer: bioSyntax.org
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# Version: v0.1
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name: bed
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file_extensions: [bed]
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scope: source.bed
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contexts:
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main:
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#Handle UCSC track line
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- match: '^track.*'
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scope: comment.bed
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# Column 1: Reference Sequence Name
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- match: '^[\S]*\t'
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scope: chr.bed
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push: start
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# Column 2: Start coordinate
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start:
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- match: ([0-9|\.]+)\b
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scope: chrStart.bed
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- match: \t
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push: end
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- match: $
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pop: true
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# Column 3: End Coordinate
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end:
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- match: ([0-9|\.]+)\b
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scope: chrEnd.bed
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- match: \t
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push: name
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- match: $
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pop: true
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# Column 4: Description / Name
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name:
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- match: '[\S]*'
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scope: string.bed
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- match: \t
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push: score
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- match: $
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pop: true
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# Column 5: Score (0-1000 scale)
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score:
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- match: \.\b
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scope: comment.bed
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- match: ([0-9])\b
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scope: grad1.bed
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- match: ([1-9][0-9])\b
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scope: grad1.bed
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- match: 1[0-9][0-9]\b
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scope: grad2.bed
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- match: 2[0-9][0-9]\b
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scope: grad3.bed
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- match: 3[0-9][0-9]\b
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scope: grad4.bed
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- match: 4[0-9][0-9]\b
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scope: grad5.bed
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- match: 5[0-9][0-9]\b
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scope: grad6.bed
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- match: 6[0-9][0-9]\b
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scope: grad7.bed
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- match: 7[0-9][0-9]\b
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scope: grad8.bed
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- match: 8[0-9][0-9]\b
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scope: grad9.bed
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- match: 9[0-9][0-9]\b
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scope: grad10.bed
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- match: ([0-9][0-9][0-9][0-9])\b
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scope: grad10.bed
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- match: \t
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push: strand
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- match: $
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pop: true
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# Column 6: Feature Strand
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strand:
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- match: \+
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scope: strandPlus.bed
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- match: \-
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scope: strandMinus.bed
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- match: \.
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scope: strandNone.bed
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- match: $
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pop: true

‎clustal.sublime-syntax

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%YAML 1.2
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---
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# Clustal syntax highlighting file
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# Maintainer: bioSyntax.org
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# Version: v0.1
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name: clustal
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# See http://www.sublimetext.com/docs/3/syntax.html
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file_extensions: [clustal]
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scope: text.clustal
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contexts:
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main:
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# Main Identifier
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- match: "^CLUSTAL.*"
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scope: comment
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# Sequence Identifier
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- match: "/[0-9]*-[0-9]*" #Optional sequence range
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scope: chrStart
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- match: "^[\\w\\.\\-\\_ ]*(?=[/ ])"
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scope: string
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# match Adenosine
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- match: "[Aa]++"
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scope: ntA
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# match Cytidine
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- match: "[Cc]++"
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scope: ntC
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# match Guanine
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- match: "[Gg]++"
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scope: ntG
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# match Thymidine/Uridine
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- match: "[TtUu]++"
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scope: ntT
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# aNy or unknown (X)
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- match: "[NnXx]++"
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scope: ntN
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# indel
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- match: "-"
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scope: ntGap

‎faidx.sublime-syntax

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%YAML 1.2
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---
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# Fasta Index (faidx) syntax highlighting file
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# Maintainer: bioSyntax.org
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# Version: v0.1
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name: faidx
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# See http://www.sublimetext.com/docs/3/syntax.html
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file_extensions: [fai,fai]
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scope: source.faidx
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# Fasta Index Filetype Description
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# NAME Name of this reference sequence
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# LENGTH Total length of this reference sequence, in bases
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# OFFSET Offset within the FASTA file of this sequence's first base
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# LINEBASES The number of bases on each line
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# LINEWIDTH The number of bytes in each line, including the newline
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contexts:
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main:
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# COLUMN 1
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- match: '^[\S]*\t'
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scope: chr.faidx
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push: contig.length
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# COLUMN 3
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- match: '(?<=\t)[\S]*\t'
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scope: numeric.faidx
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push: genomic.offset
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# COLUMN 5
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- match: '[\S]*$'
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scope: comment.faidx
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contig.length:
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# COLUMN 2
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- match: '[\S]*'
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scope: chrStart.faidx
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- match: \t
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pop: true
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genomic.offset:
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# COLUMN 4
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- match: '[\S]*'
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scope: comment.faidx
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- match: \t
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pop: true

‎fasta-clustal.sublime-syntax

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%YAML 1.2
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---
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# Fasta-Clustal syntax highlighting file
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# Maintainer: bioSyntax.org
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# Version: v0.1
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name: fasta-clustal
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# See http://www.sublimetext.com/docs/3/syntax.html
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file_extensions: [fastaa,faa]
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scope: text.fasta-clustal
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contexts:
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main:
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#positive lookbehind to match a + and a new line to any characters right after it
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#pushes it to quality
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- match: "^>.*"
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scope: string
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# match amino acids
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# Alanine (ALA)
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- match: "[Aa]"
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scope: aaA
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# Aspartate/Asparagine (ASX)
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- match: "[Bb]"
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scope: aaB
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# Cysteine (CYS)
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- match: "[Cc]"
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scope: aaC
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# Aspartate (ASP)
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- match: "[Dd]"
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scope: aaD
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# Glutamate (GLU)
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- match: "[Ee]"
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scope: aaE
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# Phenylalanine (PHE)
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- match: "[Ff]"
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scope: aaF
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# Glycine (GLY)
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- match: "[Gg]"
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scope: aaG
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# Histidine (HIS)
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- match: "[Hh]"
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scope: aaH
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# Isoleucine (ILE)
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- match: "[Ii]"
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scope: aaI
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# Lysine (LYS)
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- match: "[Kk]"
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scope: aaK
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# Leucine (LEU)
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- match: "[Ll]"
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scope: aaL
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# Methionine (MET)
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- match: "[Mm]"
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scope: aaM
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# Asparagine (ASN)
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- match: "[Nn]"
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scope: aaN
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# Proline (PRO)
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- match: "[Pp]"
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scope: aaP
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# Glutamine (GLN)
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- match: "[Qq]"
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scope: aaQ
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# Arginine (ARG)
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- match: "[Rr]"
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scope: aaR
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# Serine (SER)
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- match: "[Ss]"
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scope: aaS
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# Threonine (THE)
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- match: "[Tt]"
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scope: aaT
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# Valine (VAL)
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- match: "[Vv]"
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scope: aaV
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# Tryptophan (TRP)
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- match: "[Ww]"
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scope: aaW
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# Tyrosine (TYR)
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- match: "[Yy]"
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scope: aaY
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# Glutamate or Glutamine (GLX)
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- match: "[Zz]"
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scope: aaZ
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# any/unknown (X)
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- match: "[Xx]"
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scope: zappo.X
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# translation stop
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- match: "\\*"
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scope: comment
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# indel
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- match: "[-]"
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scope: comment

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