/usr/share/perl5/Bio/AlignIO/pfam.pm is in libbio-perl-perl 1.6.923-1.
This file is owned by root:root, with mode 0o644.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 | #
# BioPerl module for Bio::AlignIO::pfam
# based on the Bio::SeqIO:: modules
# by Ewan Birney <birney@ebi.ac.uk>
# and Lincoln Stein <lstein@cshl.org>
#
# and the SimpleAlign.pm module of Ewan Birney
#
# Copyright Peter Schattner
#
# You may distribute this module under the same terms as perl itself
# _history
# September 5, 2000
# POD documentation - main docs before the code
=head1 NAME
Bio::AlignIO::pfam - pfam sequence input/output stream
=head1 SYNOPSIS
Do not use this module directly. Use it via the L<Bio::AlignIO> class.
=head1 DESCRIPTION
This object can transform Bio::SimpleAlign objects to and from pfam flat
file databases.
=head1 FEEDBACK
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHORS - Peter Schattner
Email: schattner@alum.mit.edu
=head1 APPENDIX
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::AlignIO::pfam;
use strict;
use Bio::SimpleAlign;
use base qw(Bio::AlignIO);
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream
Returns : L<Bio::Align::AlignI> object
Args : NONE
=cut
sub next_aln {
my $self = shift;
my $entry;
my $name;
my $start;
my $end;
my $seq;
my $add;
my $acc;
my %names;
my $aln = Bio::SimpleAlign->new(-source => 'pfam');
while( $entry = $self->_readline) {
chomp $entry;
$entry =~ m{^//} && last;
if($entry !~ m{^(\S+)/(\d+)-(\d+)\s+(\S+)\s*} ) {
$self->throw("Found a bad line [$_] in the pfam format alignment");
next;
}
$name = $1;
$start = $2;
$end = $3;
$seq = $4;
$add = Bio::LocatableSeq->new('-seq' => $seq,
'-display_id' => $name,
'-start' => $start,
'-end' => $end,
'-alphabet' => $self->alphabet,
);
$aln->add_seq($add);
}
# If $end <= 0, we have either reached the end of
# file in <> or we have encountered some other error
#
return $aln if $aln->num_sequences;
return;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
if( @aln > 1 ) { $self->warn("Only the 1st pfam alignment will be output since the format does not support multiple alignments in the same file"); }
my $aln = shift @aln;
if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
next;
}
my ($namestr,$seq,$add);
my ($maxn);
$maxn = $aln->maxdisplayname_length();
foreach $seq ( $aln->each_seq() ) {
$namestr = $aln->displayname($seq->get_nse());
$add = $maxn - length($namestr) + 2;
$namestr .= " " x $add;
$self->_print (sprintf("%s %s\n",$namestr,$seq->seq())) or return;
}
$self->flush() if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;
|