[Bioperl-l] Bioperl parsing output file
DANIEL EDUARDO TORRENTE QUINTERO
dtorrente at javeriana.edu.co
Sun Feb 5 19:04:47 UTC 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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