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

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

biopython
• 7,282 views • link
updated by David W David W • written by sinanugur • sinanugur

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.

• 0 views • link
written by Adam R • Adam R

1 answer

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
• 434 views • link
written by David W David W

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.
• 175 views • link
written by Philipp Bayer Philipp Bayer

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