[Bioperl-guts-l] [Bug 2081] Error in length_aln method when parsing BLAST report with Bio::SearchIO

bugzilla-daemon at newportal.open-bio.org bugzilla-daemon at newportal.open-bio.org
Thu Aug 17 16:14:17 EDT 2006


cjfields at uiuc.edu changed:

           What    |Removed                     |Added
                 CC|                            |cjfields at uiuc.edu
             Status|NEW                         |ASSIGNED

------- Comment #3 from cjfields at uiuc.edu  2006-08-17 16:14 -------
This is what I get:


-------------------- WARNING ---------------------
MSG: There is no HSP data for hit 'ENSP00000327738'.
You have called a method (Bio::Search::Hit::GenericHit::length_aln)
that requires HSP data and there was no HSP data for this hit,
most likely because it was absent from the BLAST report.
Note that by default, BLAST lists alignments for the first 250 hits,
but it lists descriptions for 500 hits. If this is the case,
and you care about these hits, you should re-run BLAST using the
-b option (or equivalent if not using blastall) to increase the number
of alignments.

Alignment length for ENSP00000327738 is -
Alignment length for ENSP00000350182 is 250
Alignment length for ENSP00000327738 is 398

BTW, I am using the latest CVS update on WinXP, ActivePerl 5.8.8, so this bug
is present in CVS.  

One problem I can immediately is the presence of identical names for hits in
the hit table, but only one alignment is present.  This may be throwing the
hits off.  

ENSP00000350182 pep:novel clone::BX322644.8:4905:15090:-1 gene:E...   120  
ENSP00000350182 pep:novel clone::BX322644.8:4905:15090:-1 gene:E...   120  
ENSP00000327738 pep:known-ccds chromosome:NCBI36:4:189297592:189...   115  

Of note : the correct length is returned for your accession in the above output
regardless of the warning.

This may be a duplicate of bug 1986, which I suspect is due to the inclusion of
iterations for PSI-BLAST parsing (something Jason pointed out).  Would you
please attach the entire BLAST report here, or attach it to an email for me so
I can confirm this?  I'm added to the cc list for this bug now.

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