Raw content of Bio::AlignIO::msf
<![CDATA[# $Id: msf.pm,v 1.16 2002/11/26 16:34:39 jason Exp $
#
# BioPerl module for Bio::AlignIO::msf
# based on the Bio::SeqIO::msf module
# by Ewan Birney <birney@sanger.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::msf - msf 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 L<Bio::Align::AlignI> objects to and from msf flat
file databases.
=head1 FEEDBACK
=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 email or the web:
bioperl-bugs@bio.perl.org
http://bugzilla.bioperl.org/
=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::msf;
use vars qw(@ISA %valid_type);
use strict;
use Bio::AlignIO;
use Bio::SeqIO::gcg; # for GCG_checksum()
use Bio::SimpleAlign;
@ISA = qw(Bio::AlignIO);
BEGIN {
%valid_type = qw( dna N rna N protein P );
}
=head2 next_aln
Title : next_aln
Usage : $aln = $stream->next_aln()
Function: returns the next alignment in the stream. Tries to read *all* MSF
It reads all non whitespace characters in the alignment
area. For MSFs with weird gaps (eg ~~~) map them by using
$al->map_chars('~','-')
Returns : L<Bio::Align::AlignI> object
Args : NONE
=cut
sub next_aln {
my $self = shift;
my $entry;
my (%hash,$name,$str,@names,$seqname,$start,$end,$count,$seq);
my $aln = Bio::SimpleAlign->new(-source => 'gcg' );
while( $entry = $self->_readline) {
$entry =~ /\/\// && last; # move to alignment section
$entry =~ /Name:\s+(\S+)/ && do { $name = $1;
$hash{$name} = ""; # blank line
push(@names,$name); # we need it ordered!
};
# otherwise - skip
}
# alignment section
while( $entry = $self->_readline) {
next if ( $entry =~ /^\s+(\d+)/ ) ;
$entry =~ /^\s*(\S+)\s+(.*)$/ && do {
$name = $1;
$str = $2;
if( ! exists $hash{$name} ) {
$self->throw("$name exists as an alignment line but not in the header. Not confident of what is going on!");
}
$str =~ s/\s//g;
$hash{$name} .= $str;
};
}
return 0 if scalar @names < 1;
# now got this as a name - sequence hash. Lets make some sequences!
foreach $name ( @names ) {
if( $name =~ /(\S+)\/(\d+)-(\d+)/ ) {
$seqname = $1;
$start = $2;
$end = $3;
} else {
$seqname=$name;
$start = 1;
$str = $hash{$name};
$str =~ s/[^A-Za-z]//g;
$end = length($str);
}
$seq = new Bio::LocatableSeq('-seq'=>$hash{$name},
'-id'=>$seqname,
'-start'=>$start,
'-end'=>$end,
);
$aln->add_seq($seq);
# If $end <= 0, we have either reached the end of
# file in <> or we have encountered some other error
#
# if ($end <= 0) { undef $aln;}
}
return $aln;
}
=head2 write_aln
Title : write_aln
Usage : $stream->write_aln(@aln)
Function: writes the $aln object into the stream in MSF format
Sequence type of the alignment is determined by the first sequence.
Returns : 1 for success and 0 for error
Args : L<Bio::Align::AlignI> object
=cut
sub write_aln {
my ($self,@aln) = @_;
my $msftag;
my $type;
my $count = 0;
my $maxname;
my ($length,$date,$name,$seq,$miss,$pad,%hash,@arr,$tempcount,$index);
foreach my $aln (@aln) {
if( ! $aln || ! $aln->isa('Bio::Align::AlignI') ) {
$self->warn("Must provide a Bio::Align::AlignI object when calling write_aln");
next;
}
$date = localtime(time);
$msftag = "MSF";
$type = $valid_type{$aln->get_seq_by_pos(1)->alphabet};
$maxname = $aln->maxdisplayname_length();
$length = $aln->length();
$name = $aln->id();
if( !defined $name ) {
$name = "Align";
}
$self->_print (sprintf("\n%s MSF: %d Type: %s %s Check: 00 ..\n\n",
$name, $aln->no_sequences, $type, $date));
foreach $seq ( $aln->each_seq() ) {
$name = $aln->displayname($seq->get_nse());
$miss = $maxname - length ($name);
$miss += 2;
$pad = " " x $miss;
$self->_print (sprintf(" Name: %s%sLen: %d Check: %d Weight: 1.00\n",$name,$pad,length $seq->seq(), Bio::SeqIO::gcg->GCG_checksum($seq)));
$hash{$name} = $seq->seq();
push(@arr,$name);
}
# ok - heavy handed, but there you go.
#
$self->_print ("\n//\n\n\n");
while( $count < $length ) {
# there is another block to go!
foreach $name ( @arr ) {
$self->_print (sprintf("%-20s ",$name));
$tempcount = $count;
$index = 0;
while( ($tempcount + 10 < $length) && ($index < 5) ) {
$self->_print (sprintf("%s ",substr($hash{$name},$tempcount,10)));
$tempcount += 10;
$index++;
} #
# ok, could be the very last guy ;)
#
if( $index < 5) {
# space to print!
#
$self->_print (sprintf("%s ",substr($hash{$name},$tempcount)));
$tempcount += 10;
}
$self->_print ("\n");
}
$self->_print ("\n\n");
$count = $tempcount;
}
}
$self->flush if $self->_flush_on_write && defined $self->_fh;
return 1;
}
1;
]]>