[Bioperl-l] zip file

Hubert Prielinger hubert.prielinger at gmx.at
Thu Feb 9 12:32:39 EST 2006


Hi Chris,
It doesn't work with the simple input line either, but I have tried my 
script on the command line with the file scanning part and it is 
working, but it takes more than 10 minutes!!!!!!!!!!! for reading one 
file and it doesn't create the output file, so there is no output. 
Before I run the script in the eclipse IDE.
I'm trying to upgrade to bioperl 1.5.1 once more, hopefully that's the 
problem, I have installed the from bioperl.org the core, run and ext part...
the output as you got it is just fine, but nevertheless I need the 
script with the file scanning part, because I have a lot of them.

to Roger: I have tried it with different files, but always the same 
result.....reads the files, but takes them a very long time and no 
Output result file


Hubert




Chris Fields wrote:

> Hubert,
>
> I tried this script out it and it managed to parse your reports.  I  
> removed the file scanning and replaced it with a simple arg line  
> input (i.e. script.pl blast_file).   I attached one of the output files.
>
> Chris
>
>
>
> #!perl
>
> $file = shift @ARGV;
>
> use Bio::SearchIO;
> my $cutoff_len = 10;
> my $searchio = Bio::SearchIO->new( -format => 'blast',
>                                    -file   =>  $file );
> while ( my $result = $searchio->next_result() ) {
>       while( my $hit = $result->next_hit ) {
>           while(my $hsp = $hit->next_hsp) {
>             if ($hsp->length('sbjct') <= $cutoff_len) {
>                 for ($hsp->hit_string) {
>                     if (tr/K// >= 2 || tr/R// >= 2 && tr/W// >= 2 ||
>                         tr/K// == 1 && tr/R// == 1 && tr/W// >= 2) {
>                          #Print some tab-delimited data about this HSP
>                            open (bigShot, ">>BlastOutputTrial.txt") ||
>                                  die ("Could not open file. $!");
>                          #print $result->query_name, "\t";
>                          #print $hit->significance, "\t";
>                          print bigShot $hit->name, "-->";
>                          print bigShot $hit->description, "\n";
>                          print bigShot "Query:   ",
>                          $hsp->start('query'), "  ", $hsp- 
> >query_string, "  ",
>                             $hsp->end('query'), "\n";
>                          print bigShot "Seq:     ", $hsp->start('hit'),
>                             "  ", $hsp->hit_string, "  ", 
> $hsp->end('hit'), "\n";
> #                        print $hsp->rank, "\t";
> #                        print $hsp->percent_identity, "\t";
> #                        print $hsp->evalue, "\t";
> #                        print $hsp->hsp_length, "\n";
>
>                         close (bigShot);
>
>                     };
>
>
>             }
>         }
>         }
>     }
> }
>
>------------------------------------------------------------------------
>
>  
>



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