fasta_header_to_gene: extract gene symbol from fasta header string

In ftwkoopmans/msdap: Mass Spectrometry Downstream Analysis Pipeline

extract gene symbol from fasta header string

Description

GN tag contains the gene symbol. example; >sp|Q9Y2S6|TMA7_HUMAN Translation machinery-associated protein 7 OS=Homo sapiens (Human) OX=9606 GN=TMA7 PE=1 SV=1

Usage

fasta_header_to_gene(x, fasta_id_type = "uniprot")

Arguments

x	array of fasta headers
fasta_id_type	fasta type. unused argument atm

Details

uniprot headers may contain "GN=-" or no GN tag at all ! example; >sp|Q6ZSR9|YJ005_HUMAN Uncharacterized protein FLJ45252 OS=Homo sapiens (Human) OX=9606 GN=- PE=2 SV=2 example; >tr|A2ALT2|A2ALT2_MOUSE Isoform of Q03288, Nonagouti (Fragment) OS=Mus musculus OX=10090 GN=a PE=4 SV=1 example; >sp|P15252|REF_HEVBR Rubber elongation factor protein OS=Hevea brasiliensis PE=1 SV=2

ftwkoopmans/msdap documentation built on March 5, 2025, 12:15 a.m.