Adding gene names to fasta file

Question

[mm2568]

I have file 1 (a FASTA file):

>dmel_X type=golden_path_region; loc=X:2270008..2271068; ID=X; dbxref=GB:AE014298,GB:AE014298,REFSEQ:NC_004354;   release=r6.37; species=Dmel;
CTCTTTGTTAGCCTACGCTTTCTGCTGAGTTTGTTATTTTTGTCTGCTCCCCACAAGGATATTGTTACAGAGAAAAAGCT
CGAATTGAAGGGAAAATGGAGACAAATAAGAAAACCCATGACAAAGAGGAAAGTTTCAAATATGGGCAATCGAAAAAATC
GAGAAGTGAGCCAATTTTTTTTTCGCCGAGGCTCCACTGTTCCCAGCTGCATAACTGTTTTCCCTCGGCACCTCTCTTTT

>dmel_3L type=golden_path_region; loc=3L:20341634..20342694; ID=3L; dbxref=GB:AE014296,GB:AE014296,REFSEQ:NT_037436;   release=r6.37; species=Dmel;
ATTAGTATATAGGCATATGCTTAAGTCTTAGGGTCTTATGGATATGTCACTATATATATATATAATTGCATAAATAGAGA
TATAATAATAGAGGGAGATAATATATTGAAAGCTTTTAATTGCTTCATACAAATTGATGACATCTCAATATCAAATACAA
TGTTGGATTACACACAAACCGTTTATGTCAATAAGAAAATAACTAAATGGGAAGATCTTTCTATATAAGAATATATAGAG

And I have file 2 (gene names):

CG2918
Spn77Bc

How can I replace the string after the ">" in the FASTA file to have the unique gene names replace the "dmel_.....". The files are obviously longer, but the output should look like:

>CG2918 type=golden_path_region; loc=X:2270008..2271068; ID=X; dbxref=GB:AE014298,GB:AE014298,REFSEQ:NC_004354;   release=r6.37; species=Dmel;
CTCTTTGTTAGCCTACGCTTTCTGCTGAGTTTGTTATTTTTGTCTGCTCCCCACAAGGATATTGTTACAGAGAAAAAGCT
CGAATTGAAGGGAAAATGGAGACAAATAAGAAAACCCATGACAAAGAGGAAAGTTTCAAATATGGGCAATCGAAAAAATC
GAGAAGTGAGCCAATTTTTTTTTCGCCGAGGCTCCACTGTTCCCAGCTGCATAACTGTTTTCCCTCGGCACCTCTCTTTT

>Spn77Bc type=golden_path_region; loc=3L:20341634..20342694; ID=3L; dbxref=GB:AE014296,GB:AE014296,REFSEQ:NT_037436;   release=r6.37; species=Dmel;
ATTAGTATATAGGCATATGCTTAAGTCTTAGGGTCTTATGGATATGTCACTATATATATATATAATTGCATAAATAGAGA
TATAATAATAGAGGGAGATAATATATTGAAAGCTTTTAATTGCTTCATACAAATTGATGACATCTCAATATCAAATACAA
TGTTGGATTACACACAAACCGTTTATGTCAATAAGAAAATAACTAAATGGGAAGATCTTTCTATATAAGAATATATAGAG

Thank you so much!

[rpolicastro]

Are the gene names in the file the same order as the fasta entry for which it matches?

[mm2568]

Yes, the gene names in the file are in the same order as in the FASTA!

[Joe]

What is the relationship between CG2918 and dmel_X? Are they simply in order as @rpolicastro asked, or do you have some sort of mapping file?

[mm2568]

See reply above, they are in the same order - so I was hoping to iterate line by line and replace from the file to the FASTA.

Answer 1

[Joe]

Here's a biopython solution:

from Bio import SeqIO
import sys

with open(sys.argv[1], 'r') as fh:
    for name, record in zip((line for line in fh.readlines()), SeqIO.parse(sys.argv[2], 'fasta')):
        record.description = record.description.replacerecord.id+' ', '')
        record.id = name.strip()

        print(record.format('fasta'))

Run as python scriptname.py id_file.txt sequences.fasta

Note that due to a weird Biostars bug, there is meant to be a ( between and replace and record.id on line 5.

[mm2568]

This is awesome, it worked. Thank you so much for your help!