/usr/bin/bp_hmmer_to_table is in bioperl 1.7.2-2.
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
use strict;
use warnings;
=head1 NAME
bp_hmmer_to_table - turn HMMER output into tabular format
=head1 SYNOPSIS
bp_hmmer_to_table [-e evaluefilter] [-b bitscorefilter] [--header] [-o outfile] inputfile1 inputfile2 ...
=head1 DESCRIPTION
Command line options:
-e/--evalue evalue -- filter by evalue
-b/--bitscore bitscore -- filter by bitscore
--header -- boolean flag to print column header
-o/--out -- optional outputfile to write data,
otherwise will write to STDOUT
-h/--help -- show this documentation
Not technically a SearchIO script as this doesn't use any Bioperl
components but is a useful and fast. The output is tabular output.
query sequence/domain (these are flip-flopped for hmmsearch / hmmpfam)
query start
query end
domain/sequence name or PFAM accession
hit start
hit end
score
e-value
domain/sequence name (these are flip-flopped for hmmsearch / hmmpfam)
=head1 AUTHOR - Jason Stajich
Jason Stajich jason_at_bioperl-dot-org
=cut
use Getopt::Long;
my ($evalue,$bitscore,$header,$outfile);
GetOptions(
'b|bitscore|bits:f' => \$bitscore,
'e|evalue:f' => \$evalue,
'header' => \$header,
'o|out|outfile:s' => \$outfile,
'h|help' => sub { exec('perldoc',$0); exit; }
);
my $outfh;
if( $outfile ) {
open $outfh, '>', $outfile or die "Could not write file '$outfile': $!\n";
} else {
$outfh = \*STDOUT;
}
my @fields = qw(QNAME QSTART QEND HACCESSION HSTART HEND SCORE EVALUE HNAME);
if( $header ) {
print $outfh join("\t", @fields), "\n";
}
my %dat;
while(<>) {
if( s/^Query(\s+(sequence|HMM))?:\s+// ) {
s/\s+$//;
$dat{'Query'} = $_;
} elsif( /^Parsed for domains:/ ) {
my $ready = 0;
while(<>) {
if(/^Model|Sequence\s+Domain/ ) { $ready = 1; }
elsif( $ready && /^\-\-/) { $ready = 2; }
elsif( /^Alignments of/ ) { undef %dat; last; }
elsif( $ready == 2 ) {
if( my ($n,$domainnum,$domainct, @vals) =
(m!^(\S+)\s+ # domain name
(\d+)\/(\d+)\s+ # num/num (ie 1 of 2)
(\d+)\s+(\d+).+? # sequence start and end
(\d+)\s+(\d+)\s+ # hmm start and end
\S+\s+ # []
(\S+)\s+ # score
(\S+) # evalue
\s*$!ox) ) {
next if( defined $bitscore && $vals[4] < $bitscore );
next if (defined $evalue && $vals[5] > $evalue);
print $outfh join("\t",
$dat{'Query'},
$vals[0], $vals[1],
$n,
$vals[2],$vals[3],
$vals[4],$vals[5],
$n),"\n";
}
}
}
}
}
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