[BioPython] How can I retreive FASTA sequences from NCBI
Srinivas Iyyer
srini_iyyer_bio at yahoo.com
Sat Apr 1 18:13:16 UTC 2006
Hi ,
I have 151,204 GenBank Accession IDs.
I want to retreive FASTA sequences from NCBI and
compile them for my local blast.
I am unable to get fasta sequences. I do not
understand.
Could any one please help me.
my code:
>>> mylis
['AA035383', 'AA971406', 'N98563']
parser = Fasta.RecordParser()
iterator = Fasta.Iterator(mylis,parser)
rec = iterator.next()
rec = iterator.next()
>>> rec
>>>
rec is empty :-(
Accession IDs are not GIs. They are GenBank accession
Ids.
I do not want sequences in GenBank (long format). I
want them in FASTA sequence format.
Could any one pleast help me.
Thanks
Srini
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