fasta-zappo.sublime-syntax

%YAML 1.2
---
# Fasta-Zappo syntax highlighting file
# Maintainer: bioSyntax.org
# Version: v0.1
name: fasta-zappo
# See http://www.sublimetext.com/docs/3/syntax.html
file_extensions: [fastza]
scope: text.fasta-zappoa


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: zappoA

    # Aspartate/Asparagine (ASX)
    - match: "[Bb]"
      scope: zappoB

    # Cysteine (CYS)
    - match: "[Cc]"
      scope: zappoC

    # Aspartate (ASP)
    - match: "[Dd]"
      scope: zappoD

    # Glutamate (GLU)
    - match: "[Ee]"
      scope: zappoE

    # Phenylalanine (PHE)
    - match: "[Ff]"
      scope: zappoF

    # Glycine (GLY)
    - match: "[Gg]"
      scope: zappoG

    # Histidine (HIS)
    - match: "[Hh]"
      scope: zappoH

    # Isoleucine (ILE)
    - match: "[Ii]"
      scope: zappoI

    # Lysine (LYS)
    - match: "[Kk]"
      scope: zappoK

    # Leucine (LEU)
    - match: "[Ll]"
      scope: zappoL

    # Methionine (MET)
    - match: "[Mm]"
      scope: zappoM

    # Asparagine (ASN)
    - match: "[Nn]"
      scope: zappoN

    # Proline (PRO)
    - match: "[Pp]"
      scope: zappoP

    # Glutamine (GLN)
    - match: "[Qq]"
      scope: zappoQ

    # Arginine (ARG)
    - match: "[Rr]"
      scope: zappoR

    # Serine (SER)
    - match: "[Ss]"
      scope: zappoS

    # Threonine (THE)
    - match: "[Tt]"
      scope: zappoT

    # Valine (VAL)
    - match: "[Vv]"
      scope: zappoV

    # Tryptophan (TRP)
    - match: "[Ww]"
      scope: zappoW

    # Tyrosine (TYR)
    - match: "[Yy]"
      scope: zappoY

    # Glutamate or Glutamine (GLX)
    - match: "[Zz]"
      scope: zappoZ

    # any/unknown (X)
    - match: "[Xx]"
      scope: zappoX

    # translation stop
    - match: "\\*"
      scope: comment

    # indel
    - match: "[-]"
      scope: comment