Bioperl: Blast Parsing Error

[hilmar.lapp@pharma.Novartis.com]

Alan,

I've encountered this bug as well with the main trunk. I succeeded for single
BLAST reports by moving this fix to the very end of the block enclosed by

            if($Blast->{'_blast_count'} > 1) {

          }

According to the original bug-report from the Incyte guys, they tried to fix
multiple Blast reports with some containing no hits, so maybe my change would
still fail for multiple reports with the first having no hits (when gets
$Blast->{'_blast_count'} greater than 1?). Anyway, as I'm not sure of the
particular dependencies I haven't dared to apply a fix to the repository yet,
but maybe Steve or someone who dares can have a look.

     Hilmar






Alan Williams <alan@neomorphic.com> on 27.05.2000 00:42:27

To:   Bioperl <vsns-bcd-perl@lists.uni-bielefeld.de>
cc:    (bcc: HILMAR LAPP/PH/Novartis)

Subject:  Bioperl: Blast Parsing Error





I am getting exceptions thrown when trying to parse blast files with no
hits. The exception is due to _parse_header failing because the $data
passed to it doesn't have the whole blast report but only from the "No
Hits" string on.

The parsing error is due to the following "fix" in Blast.pm:

 # Incyte_Fix:   Nasty Invisible Bug.
 # Records in blast report are delimited by '>', but... when
 #  there are no hits for a query, there won't be a '>'.  That
 #  causes several blast reports to run together in the data
 #  passed to this routine.  Need to get rid of non-hits in data
 if ($data =~ /.+(No hits? found.+Sequences.+)/so) {
     $data = $1;
 }
 # End Incyte_Fix

A possible fix might look like:

 if ($data =~ /(T?BLAST[NPX].+No hits? found.+Sequences.+)/so) {

This is in the 0.61 tarball. Sorry if this has already been reported.


-Alan

---------------------------------
Alan Williams
Neomorphic, Inc.
Alan@Neomorphic.com
510-981-8513
---------------------------------

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