Biopython: Change Sequence Id And Print Out New Sequence

Question

[QVINTVS_FABIVS_MAXIMVS]

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

Answer 1

[Neilfws]

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.

[thekswenson]

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.