/usr/bin/bp_search2table is in bioperl 1.6.923-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
=head1 NAME
bp_search2table - turn SearchIO parseable reports into tab delimited format like NCBI's -m 9
=head1 SYNOPSIS
bp_search2table -f fasta -i file.FASTA -o output.table
=head1 DESCRIPTION
Turn SearchIO reports into a tabular format like NCBI's -m 9 output.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR
Jason Stajich jason_at_bioperl-dot-org
=cut
use strict;
use warnings;
use Bio::SearchIO;
use Getopt::Long;
my ($format, $file,$output) = ('blast');
GetOptions(
'f|format:s' => \$format,
'i|input:s' => \$file,
'o|output:s' => \$output);
if( @ARGV ) {
$file = shift;
}
my $in = Bio::SearchIO->new(-format => $format,
-file => $file);
my $out;
if( $output ) {
open($out,">$output") || die "cannot open $output for writing";
} else {
$out = \*STDOUT;
}
while( my $r = $in->next_result ) {
while( my $hit = $r->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
my $mismatchcount = $hsp->length('total') -
($hsp->num_conserved + $hsp->gaps('total'));
print $out join("\t", ( $r->query_name,
$hit->name,
sprintf("%.2f",$hsp->percent_identity),
$hsp->length('total'),
$mismatchcount,
$hsp->gaps('total'),
# flip start/end on rev strand
$hsp->query->strand < 0 ?
( $hsp->query->end,
$hsp->query->start ) :
( $hsp->query->start,
$hsp->query->end ),
$hsp->hit->strand < 0 ?
( $hsp->hit->end,
$hsp->hit->start ) :
( $hsp->hit->start,
$hsp->hit->end ),
$hsp->evalue,
# chance this to $hsp->sw_score
# if you would rather have that
# it will only work for FASTA parsing though!
$hsp->bits)),"\n";
}
}
}
|