Biopython: Is It Possible To Update Only Sequence In A Seqrecord Object?

Question

[sinanugur]

Well I know sequence objects are immutable, but why cant we assign a new sequence to a SeqRecord object without changing any other data.

[Adam R]

If you are hitting an error relating to letter annotations (e.g. "You must empty the letter annotations first!"), you can copy them to a temporary dict object while you modify the seq, clear them, and then copy them back to the SeqRecord afterwards.

Answer 1

[David W]

Yep:

from Bio import Seq
from Bio import SeqRecord

rec = SeqRecord.SeqRecord(id='test', description='', seq=Seq.Seq('ATTGA'))
print rec.format('fasta')

#>test
#ATTGA

rec.seq = Seq.Seq('ATTGG')
print rec.format('fasta')

#>test
#ATTGG

[Philipp Bayer]

I just wanted to post something similar - it's important that the new sequence 'ATTGG' is an object of class Seq, not a string, because then you'll get (at least on my system with Python 2.7.5 and BioPython 1.62b)

SeqRecord (id=test) has an invalid sequence.