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" bioSyntax
" Syntax Highlighting for Computational Biology
" =========================================================
" https://bioSyntax.org || info@bioSyntax.org || GPLv3
"
" Filetype: Fasta-ORF
" Extensions: [no default set]
" Version: v0.1
"
" Description: Nucleotide Fasta highlighting open reading
" frames (ORFs). Will highlight from first
" 'ATG' to first STOP codon.
if exists("syntax_on")
syntax reset
colorscheme bioSyntax
set nowrap
endif
syntax match headerbw ">.*$"
" ORF begins at first ATG
syntax match Start '\v[Aa]\n?[Tt]\n?[Gg]\n?' nextgroup=codon
" codon shade 1
syntax match codon '\v[AaTtGgCc]{-3}\n|
\[AaTtGgCc]{-3}|
\[AaTtGgCc\n]{-4}'
\ contained nextgroup=Opal,Ochre,Amber,codon2
" codon shade 2
syntax match codon2 '\v[ATGCatgc]{-3}\n|
\[AaTtGgCc]{-3}|
\[AaTtGgCc\n]{-4}'
\ contained nextgroup=Opal,Ochre,Amber,codon
" Stop codons: TGA | TAA | TAG
syntax match Opal '\v([Tt]\n?[Gg]\n?[Aa]|>)' contained
syntax match Ochre '\v([Tt]\n?[Aa]\n?[Aa]|>)' contained
syntax match Amber '\v([Tt]\n?[Aa]\n?[Gg]|>)' contained
"syntax cluster Stops contains=Opal,Ochre,Amber
" " Highlighting / Theme Control
" =========================================================
highlight link Start ntA
highlight link codon numeric
highlight link codon2 numeric2
highlight link Opal ntC
highlight link Ochre ntC
highlight link Amber ntC
|
