[BioPython] Blast/NCBIWWW parser Problems
±è½Â¹ü
picxenk@dreamwiz.com
Fri, 20 Sep 2002 16:39:08 +0900 (KST)
--0-1892510473-1032507549=:12887
Content-Type: TEXT/PLAIN; CHARSET=US-ASCII
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
# by picxenk
# picxenk@dreamwiz.com
# picxenk@xenbio.net
# http://xenbio.net
# http://squeak.wo.to
-------------------------------------------------
DreamWiz Free Mail @ http://www.dreamwiz.com/
DreamSearch Click the world!!! http://search.dreamwiz.com/
--0-1892510473-1032507549=:12887
Content-Type: TEXT/HTML; CHARSET=US-ASCII
<HTML>
<BODY>
<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
<BR></BODY>
</HTML>
<BR>
<BR># by picxenk
<BR># picxenk@dreamwiz.com
<BR># picxenk@xenbio.net
<BR># <A HREF="http://xenbio.net" TARGET=_blank>http://xenbio.net</A>
<BR># <A HREF="http://squeak.wo.to" TARGET=_blank>http://squeak.wo.to</A>
<BR>
<BR>
<BR>
<a HREF="http://www.dreamwiz.com/" TARGET=_blank><img SRC="http://mail.dreamwiz.com/picxenk/cgi-bin/receive_check.cgi?mailbox=Sent&uid_validity=00000000000964001213&uid=00000000000000000426,X00000&key=e1013075dced14119beeec2eff1d7fd1" BORDER="0"></a> <FONT SIZE=2><B>Your life on the net</FONT></B><br>
--0-1892510473-1032507549=:12887--