/usr/bin/bp_nrdb is in bioperl 1.6.924-3.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
# Author Jason Stajich <jason-at-bioperl-dot-org>
#
# Make a non-redundant database based on sequence (not on ID!)
# This script is still in progress but is intended to mimic what
# Warren Gish's nrdb does
# It requires that Digest::MD5 is installed (for now)
=head1 NAME
bp_nrdb.PLS - a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases
=head1 SYNOPSIS
Usage:
bp_nrdb.PLS [options] file1 file2 file3
Alternative usage
bp_nrdb.PLS -p [options] file1 id1 file2 id2 file3 id3
=head1 DESCRIPTION
This script will create a unique database of sequences
(quasi-nonredundant). The options are:
-o filename - the filename the db is written (STDOUT by default)
-a filename - the filename to append the db to
-l# - minimum required sequence length
-i - do not check for duplicates
-n# - max number of descriptions to report per seq
-d# - delimiter to use between consecutive descriptions
-p - use database id prefixes from command line
=head1 AUTHOR
Jason Stajich, jason-at-bioperl-dot-org
=cut
use strict;
use warnings;
use Bio::SeqIO;
use Getopt::Long;
use Digest::MD5 qw(md5_hex);
my ($output,$append,$min_len,
$no_duplicate_check,$desc_count,
$delimiter, $expect_prefixes,$help);
$delimiter = ';';
GetOptions(
'o|output:s' => \$output,
'a|append:s' => \$append,
'n:s' => \$desc_count,
'l:s' => \$min_len,
'd:s' => \$delimiter,
'p' => \$expect_prefixes,
'i' => \$no_duplicate_check,
'h' => \$help,
);
die("must supply a positive integer for -d") if ( defined $desc_count &&
( $desc_count !~ /^\d+$/ ||
$desc_count < 1) );
die("must supply a positive integer for -l") if ( defined $min_len &&
( $min_len !~ /^\d+$/ ||
$min_len < 1) );
my @files;
if( $help || ! @ARGV ) {
exec('perldoc',$0);
exit(0);
}
while( @ARGV ) {
my ($file, $id) = (undef,'');
if( $expect_prefixes ) {
($file,$id) = (shift @ARGV, shift @ARGV);
if( ! $id ) {
die("Must provide 'name id' pairing of dbfile and id");
}
} else {
$file = shift @ARGV;
}
push @files, [ $file,$id];
}
my $out;
if( $append ) {
$out = new Bio::SeqIO(-file => ">>$append");
} elsif( $output ) {
$out = new Bio::SeqIO(-file => ">$output");
} else {
$out = new Bio::SeqIO(); # use STDOUT
}
my %unique;
my %seqcount;
my $counter = 0;
foreach my $pair ( @files ) {
my ($file,$id) = @$pair;
my $in = new Bio::SeqIO(-file => $file);
while( my $seq = $in->next_seq ) {
next if defined $min_len && $seq->length < $min_len;
if( $id ) {
$seq->display_id("$id:".$seq->display_id);
}
my $s = lc($seq->seq());
my $md5sum = md5_hex($s);
if( $no_duplicate_check ) {
$md5sum = $counter++;
}
if( defined $unique{$md5sum} ) {
$seqcount{$md5sum}++;
next if defined $desc_count && $seqcount{$md5sum++} > $desc_count;
my $desc = $unique{$md5sum}->description;
my $id2 = sprintf("%s %s:%s %s",$delimiter,
$id,$seq->display_id,$seq->description);
$unique{$md5sum}->desc($desc . $id2);
} else {
$unique{$md5sum} = $seq;
}
}
}
foreach my $seq ( values %unique ) {
$out->write_seq($seq);
}
__END__
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