[Bioperl-l] Broken RemoteBlast fixes

Leo, Paul (NIH/NHGRI) pleo at mail.nih.gov
Thu Sep 22 11:02:52 EDT 2005

So I come back from a "bio-perl break" and my code is spitting the dummy.


RemoteBlast was DOA.


I see there is some discussion about this in Septembers mailing list
archives; the fixes that worked for me were changing:

Scott Markel : ( $size > 1000 ) to ( $size > 2000 ) in RemoteBlast.pm


paul.boutros : line 1145 of Bio\SearchIO\blast.pm this way:
-1145:        if( /^((Query|Sbjct):\s+(\-?\d+)\s*)(\S+)\s+(\-?\d+)/ ) {
+1145:        if( /^((Query|Sbjct):{0,1}\s+(\-?\d+)\s*)(\S+)\s+(\-?\d+)/ ) {
I had to make BOTH changes for it to work. 
Note that BioPerl 1.4 form ActiveState does not have these changes and does
not work which I'm sure will confuse the hell out of any new users!

Question: are these the best fixes to use, are these modules working in 1.5?




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