clustal.sublime-syntax

%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