[Bioperl-l] Bioperl parsing output file

DANIEL EDUARDO TORRENTE QUINTERO dtorrente at javeriana.edu.co
Sun Feb 5 14:04:47 EST 2012


i need some help in this script


#!/usr/bin/perl
use Bio::SearchIO;

$report_obj = new Bio::SearchIO(-format => 'blast',
                     -file   => 'C:\blast-2.2.25+\Lib3_consensus_dbAt.xml');
    while( $result = $report_obj->next_result ) {
        while( $hit = $result->next_hit ) {
           while( $hsp = $hit->next_hsp ) {
              if ( $hsp->evalue <= 0.00001 ) {
                   print "Hit\t", $hit->name, "\n", "Length\t", $hsp->length('total'),
                   "\n", "Percent_id\t",
                   $hsp->percent_identity, "\n",$result>query_name(),;  }  } } }


I want to export the results of de perl script on a file but i dont know how..... i tried to use all the  Bio::SearchIO::Writer<http://www.bioperl.org/wiki/Module:Bio::SearchIO::Writer> methods but i cant make it work with this script.






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