This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Biopython: Change Sequence Id And Print Out New Sequence

I'm learning biopython and I'm having trouble with reassigning the seq_record.id variable for my sequence.

from Bio import SeqIO

for seq_record in SeqIO.parse(file, "fasta"):
        seq_record.id = name[0] #name[0] is the new ID
        printseq_record.id)
        SeqIO.write(seq_record, "/Users/bucephalus/Desktop/nc_pimps/raw/"+name[0]+".fas", "fasta")

When the program prints it prints what I want

12345-123
12346-123
...

But when I open my files the headers are like

>12345-123 gi|1906382|gb|K03455.1|HIVHXB2CG

HELP PLOX

Tusen takk

biopython python fasta
• 7,323 views • link
updated by Ram Ram • written by QVINTVS_FABIVS_MAXIMVS QVINTVS_FABIVS_MAXIMVS

1 answer

Everything is as it should be.

In fasta format, the ID is the part immediately after the ">" and before a whitespace. So when you ask for seq_record.id, that is what you see.

When you write out a new fasta file, you get the ID plus whatever comes after the whitespace. The text after the whitespace is termed the description. It is not part of the ID.

• 121 views • link
written by Neilfws Neilfws

If you change just the description, then the fasta file contains the old id and then the new description. If both the old id and then the new description are changed identically, then you get the effect that you desire.

• 1 views • link
updated by Ram Ram • written by thekswenson • thekswenson

Log in to answer this question.

More posts like this