[BioPython] Sequence from Fasta
Peter
biopython at maubp.freeserve.co.uk
Mon Jun 30 09:19:16 UTC 2008
Which version of Biopython do you have? I'm guessing Biopython 1.44.
On older versions you would have to do explicitly turn the Seq into a
string.
Does this work:
from Bio import SeqIO
handle = open("ls_orchid.fasta")
for seq_record in SeqIO.parse(handle, "fasta") :
print seq_record.id
print seq_record.seq.tostring()
print len(seq_record.seq)
handle.close()
Since Biopython 1.45, doing str(...) on a Seq object gives you the
sequence in full as a plain string. When you do a print this happens
implicitly.
Peter
P.S. For the implementation, str(object) calls the object.__str__() method.
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