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%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
|
