right now I am getting into the basics of Biopython, working through the Tutorial.
5.3.2 Parsing SwissProt sequences from the net
In this chapter following piece of code doesn't work for me:
from Bio import ExPASy from Bio import SeqIO with ExPASy.get_sprot_raw("O23729") as handle: seq_record = SeqIO.read(handle, "swiss") printseq_record.id) printseq_record.name) print(seq_record.description) print(repr(seq_record.seq)) print("Length %i" % len(seq_record)) print(seq_record.annotations["keywords"])
This is what I get at the very beginning and end of the error message:
AssertionError Traceback (most recent call last) <ipython-input-2-87002128e48c> in <module> 2 from Bio import SeqIO 3 with ExPASy.get_sprot_raw("O23729") as handle: ----> 4 seq_record = SeqIO.read(handle, "swiss") 5 printseq_record.id) 6 printseq_record.name)
AssertionError: /note="Chalcone synthase 3"
I am a beginner so please bear with me :). I think the file can actually be obtained from ExPASy but
seq_record = SeqIO.read(handle, "swiss")
is where the problem starts Why is it not possible to get seq_record objects from the ExPASy file, do I have to change the
SeqIO.read() function? When I use
SeqIO.parse() this error returns:
AttributeError: 'generator' object has no attribute 'id'
Hope to get this solved with your help, folks! Keep it up