Bioperl: Blast Parsing Error

[Alan Williams]

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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