[Bioperl-l] bl2seq error when no alignment

Julio Fernandez Banet julipao at terra.es
Tue Jun 3 16:43:29 EDT 2003

I'm parsing bl2seq using BPbl2seq. My problem comes when only of my
sequences didn't give me any alignment and the program crashes with the
following error message:
Can't call method "nextHSP" on unblessed reference at
/Library/Perl/Bio/Tools/BPbl2seq.pm line 242, <GEN79> line 31.

I place lots of check lines in my code and I the program crashes when
reaching this line:
 while(my $hsp = $report->next_feature) {

Should I change or add something so the program doesn't crash when there's
no sequence alignment?.

Thanks a lot for your help.

The file that give the error is:

Query= ABIX Testing -- no comment
         (762 letters)

Lambda     K      H
    1.37    0.711     1.31

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 0
Number of Sequences: 0
Number of extensions: 0
Number of successful extensions: 0
Number of sequences better than 10.0: 0
length of query: 762
length of database: 53,522
effective HSP length: 13
effective length of query: 749
effective length of database: 52,612
effective search space: 39406388
effective search space used: 39406388
T: 0
A: 30
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 11 (22.3 bits)


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