[BioPython] Blast/NCBIWWW parser Problems

±è½Â¹ü picxenk@dreamwiz.com
Fri, 20 Sep 2002 16:39:08 +0900 (KST)


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Hi.

Maybe.. Blast format changed again.

I think, in NCBIWWW/_scan_one_pairwise_alignment method 
"read_and_call_until(uhandle, consumer.noevent, contain='<PRE>')" is needed before read_and_call(....<PRE>).

and in NCBIWWW/_scan_alignment_header method
alignment header can be three lines.
so Parser can not find "Length =" string.

check it please.

I used Python 2.2 and biopython-1.00a4, of course with a updated NCBIWWW.py in CVS


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<BR>Hi.
<BR>
<BR>Maybe.. Blast format changed again.
<BR>
<BR>I think, in NCBIWWW/_scan_one_pairwise_alignment method 
<BR>"read_and_call_until(uhandle, consumer.noevent, contain='<PRE>')" is needed before read_and_call(....<PRE>).

and in NCBIWWW/_scan_alignment_header method
alignment header can be three lines.
so Parser can not find "Length =" string.

check it please.

I used Python 2.2 and biopython-1.00a4, of course with a updated NCBIWWW.py in CVS


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