/usr/bin/bp_search2alnblocks is in bioperl 1.6.924-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
# Author: Jason Stajich <jason-at-bioperl-dot-org>
# Description: Turn SearchIO parseable report(s) into a set of Aligned blocks
#
=head1 NAME
bp_search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks
=head1 SYNOPSIS
bp_search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
blast file2.blast ...> out.fas
=head1 DESCRIPTION
This script will parse and filter BLAST (or other formats
L<Bio::SearchIO> can parse) output and format the alignment as blocks
of alignments based on the HSPs. Note this can only work if the input
file parsed contains the necessary.
Typically this can be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes (E.Rivas).
=head1 OPTIONS
--maxevalue Maximum E-value for an HSP
--minevalue Minimum E-value for an HSP
--minlen Minimum length of an HSP [default 0]
--maxid Maximum Percent Id [default 100]
(to help remove sequences which are really close)
--minid Minimum Percent Identity for an HSP [default 0]
-i/--input An optional input filename (expects input on STDIN by default)
-o/--output An optional output filename (exports to STDOUT by default)
-f/--format Specify a different Search Alignment format-
{fasta, axt, waba, blast, blastxml} are all permitted
although the format must have actual alignment
sequence for this script to work
See L<Bio::SearchIO> for more information.
-of/--outformat Output format for the alignment blocks, anything
L<Bio::AlignIO> supports.
-v/--verbose Turn on debugging
=head1 AUTHOR - Jason Stajich
Jason Stajich, jason-at-bioperl-dot-org.
=cut
use strict;
use warnings;
use Bio::SearchIO;
use Bio::AlignIO;
use Math::BigFloat;
use Getopt::Long;
my $Usage = 'search2alnblocks --minid PERCENTID --minlen LEN --maxevalue EVALUE file1.blast file2.blast ... > blocks.fas';
my ($min_id,$min_len,$max_id,$max_len,$max_evalue,$min_evalue,$format,
$outformat,$verbose,$input,$output);
$min_id = 0;
$max_evalue = 0;
$min_evalue = undef;
$min_len = 0;
$format = 'blast';
$outformat= 'fasta';
GetOptions(
'minid:s' => \$min_id,
'maxid:s' => \$max_id,
'minlen:s' => \$min_len,
'maxlen:s' => \$max_len,
'minevalue:s' => \$min_evalue,
'maxevalue:s' => \$max_evalue,
'f|format:s' => \$format,
'i|input:s' => \$input,
'o|output:s' => \$output,
'of|oformat:s' => \$outformat,
'v|verbose' => \$verbose,
'h|help' => sub { system('perldoc', $0);
exit(0) },
);
$max_evalue =~ s/^e/1e/;
# if $input is undef then will read from STDIN
my $parser = new Bio::SearchIO(-format => $format,
-file => $input,
-verbose=> $verbose);
my $out;
if( $output ) {
$out = new Bio::AlignIO(-format => $outformat,
-file => ">$output");
} else {
$out = new Bio::AlignIO(-format => $outformat);
}
my $id = 1;
while( my $r = $parser->next_result ) {
while( my $hit = $r->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
my $hsplen = $hsp->length('total');
next if( $min_len && $hsplen < $min_len);
my $pid = $hsp->percent_identity;
next if( ($min_id && $pid < $min_id) ||
($max_id && $pid > $max_id ) );
next if( defined $min_evalue &&
$hsp->evalue > $min_evalue );
next if( $max_evalue &&
$hsp->evalue < $max_evalue);
$verbose && $hsp->verbose($verbose);
my $aln = $hsp->get_aln();
my @seqs;
foreach my $seq ( $aln->each_seq ) {
if( $seq->display_id =~ /(\S+)[\/\_](\d+)\-(\d+)/ ) {
$seq->display_id($1);
$seq->start($seq->start + $2 - 1);
$seq->end($seq->end + $2 - 1);
}
$seq->description(sprintf("PID=%.2f LEN=%d HSP=%d",
$pid,$hsplen,$id));
push @seqs, $seq;
}
$aln = new Bio::SimpleAlign();
$aln->add_seq(shift @seqs);
$aln->add_seq(shift @seqs);
$id++;
$out->write_aln($aln);
}
}
}
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