fasta-clustal.sublime-syntax

%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