How to replace Accession Number for GI in a fasta header

Question

[marcelavillegasp]

Hi everyone!

I need help with something. I am very new to bioinformatics.

I have a fasta file with 32K reference sequences for an X gene. The headers are the Accession numbers, but I need to change them for the GI.

I already have a txt file with the GI corresponding to each Accession Number (So I think I already did the hardest part) but now I need to combine this information and change de headers of my fasta for the GI of each sequence.

I've tried with this script:

fasta= open('seq.fa')
newnames= open('newnames.txt')
newfasta= open('seqnew.fa', 'w')

for line in fasta:
    if line.startswith('>'):
        newname= newnames.readline()
        newfasta.write(newname)
    else:
        newfasta.write(line)

fasta.close()
newnames.close()
newfasta.close()

But this is changing the headers for the corresponding raw of the txt. How can I change this Accession number for the GI that I already have in a tabulated txt file?

My txt file is:

Accession Number         GI
AB079690        22212526
EF394164        126842524
EU113233        157361205

Thanks

[Matt Shirley]

Looks like you might have an answer here: Fasta sequence replacement based on header name

Answer 1

[Matt Shirley]

If you're interested in using a library you can take advantage of the key_function argument in pyfaidx:

[marcelavillegasp]

Many thanks!. I will try this