/usr/bin/bp_mrtrans 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 99 100 101 102 103 104 105 106 107 | #!/usr/bin/perl
eval 'exec /usr/bin/perl -S $0 ${1+"$@"}'
if 0; # not running under some shell
use strict;
# Author: Jason Stajich <jason-at-bioperl-dot-org>
# Description: Perl implementation of Bill Pearson's mrtrans
# to project protein alignment back into cDNA coordinates
#
=head1 NAME
bp_mrtrans - implement a transformer of alignments from protein to mrna coordinates
=head1 SYNOPSIS
Usage:
bp_mrtrans -i inputfile -o outputfile [-if input format] [-of output format] [-s cDNA sequence database] [-sf cDNA sequence format] [-h]
=head1 DESCRIPTION
This script will convert a protein alignment back into a cDNA. Loosely
based on Bill Pearson's mrtrans.
The options are:
-o filename - the output filename [default STDOUT]
-of format - output sequence format
(multiple sequence alignment)
[default phylip]
-i filename - the input filename [required]
-if format - input sequence format
(multiple sequence alignment)
[ default clustalw]
-s --seqdb filename - the cDNA sequence database file
-sf --seqformat - the cDNA seq db format (flatfile sequence format)
-h - this help menu
=head1 AUTHOR
Jason Stajich, jason-at-bioperl-dot-org
=cut
use strict;
use warnings;
use Bio::Align::Utilities qw(aa_to_dna_aln);
use Bio::AlignIO;
use Bio::SeqIO;
use Getopt::Long;
# TODO - finish documentation,
# - add support for extra options in output alignment formats
# such as idnewline in phylip out to support Molphy input files
my ($iformat,$seqformat,$oformat,$seqdb,$input,$output) = ('clustalw','fasta',
'phylip');
my ($help,$usage);
$usage = "usage: bp_mrtrans.pl -i prot_alignment -if align_format -o out_dna_align -of output_format -s cDNA_seqdb -sf fasta\n".
"defaults: -if clustalw
-of phylip
-sf fasta\n";
GetOptions(
'if|iformat:s' => \$iformat,
'i|input:s' => \$input,
'o|output:s' => \$output,
'of|outformat:s'=> \$oformat,
's|seqdb|db:s' => \$seqdb,
'sf|seqformat:s'=> \$seqformat,
'h|help' => sub{ exec('perldoc',$0);
exit(0)
},
);
$input ||= shift;
$seqdb ||= shift;
$output ||= shift;
if( ! defined $seqdb ) {
die("cannot proceed without a valid seqdb\n$usage");
}
if( ! defined $input ) {
die("cannot proceed without an input file\n$usage");
}
my $indb = new Bio::SeqIO(-file => $seqdb,
-format=>$seqformat);
my %seqs;
while( my $seq = $indb->next_seq ) {
$seqs{$seq->id} = $seq;
}
my $in = new Bio::AlignIO(-format => $iformat,
-file => $input);
my $out = new Bio::AlignIO(-format => $oformat,
-idlength => 22,
-interleaved => 0,
defined $output ? (-file => ">$output") : () );
while( my $aln = $in->next_aln ) {
my $dnaaln = aa_to_dna_aln($aln,\%seqs);
$dnaaln->set_displayname_flat(1);
$out->write_aln($dnaaln);
}
__END__
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