[Bioperl-l] [BULK] can't parse blast file anymore

[Hubert Prielinger]

hi,
I have corrected that and now I finally I got a few error messages:

blast.pm: unrecognized line Reference: Altschul, Stephen F., Thomas L. 
Madden, Alejandro A. Schäffer,
blast.pm: unrecognized line Jinghui Zhang, Zheng Zhang, Webb Miller, and 
David J. Lipman
blast.pm: unrecognized line (1997), "Gapped BLAST and PSI-BLAST: a new 
generation of
blast.pm: unrecognized line protein database search programs", Nucleic 
Acids Res. 25:3389-3402.
blast.pm: unrecognized line RID: 1137529800-24476-151611170370.BLASTQ1

after that line it stops without terminating....


Torsten Seemann wrote:
> Hubert Prielinger wrote:
>> ok, thanks
>> I have submitted the bug
>> bug #1994
>
> This is a line from the script you sent to Bugzilla:
>
> my $search = new Bio::SearchIO (
> -verbose => 1,-format => 'blast', -file => $file)
> or die "could not open blast report" if not defined my $search;
>
> Althoygh syntactically correct, I don't think it is doing what you want.
> Please change it to this:
>
> my $search = new Bio::SearchIO(-format => 'blast', -file => $file) or 
> die "could not open blast report";
>
> or alternatively, this:
>
> my $search = new Bio::SearchIO(-format => 'blast', -file => $file);
> if (not defined $search) {
>   die "could not open blast report";
> }
>
> and let us know what happens.
>
> all the example output you have supplied still suggests that 
> Bio::SearchIO can not load or parse your blast report.
>