bioSyntax-sublime/fasta-hydro.sublime-syntax at master · bioSyntax/bioSyntax-sublime · GitHub

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


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: hydroA

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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