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executable file 35 lines (29 sloc) 779 Bytes
#!/usr/bin/perl
use strict;
use Bio::SearchIO;
use Getopt::Long;
use Benchmark;
my ($infile,$outfile,$verbose);
GetOptions(
'i|input:s' => \$infile,
'o|output:s' => \$outfile,
'v|verbose' => \$verbose,
);
$infile = shift unless $infile;
my $in = new Bio::SearchIO(-format => 'waba',
-file => $infile, #comment out to read from STDIN
#-fh => \*ARGV, # uncomment to read from STDIN
-verbose => $verbose);
my $out;
if( defined $outfile) {
$out = new Bio::Tools::GFF(-file => ">$outfile");
} else {
$out = new Bio::Tools::GFF(-verbose => $verbose);
}
while( my $r = $in->next_result ) {
while( my $hit = $r->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
$out->write_feature($hsp);
}
}
}