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Summary

Bio::AlignIO::msf - msf sequence input/output stream

Package variables

Included modules

Inherit

Bio::AlignIO

Synopsis

Do not use this module directly. Use it via the Bio::AlignIO class.

Description

This object can transform Bio::Align::AlignI objects to and from msf
flat file databases.

Methods

Methods description

 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
           $aln->map_chars('~','-')
 Returns : Bio::Align::AlignI object
 Args    : NONE

 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    : Bio::Align::AlignI object

Methods code

BEGIN {

	%valid_type = qw( dna N rna N protein P );

}

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 =~ m{//} && 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;
	    $str =~ s/~/-/g;
	    $hash{$name} .= $str;
	};
    }

    # return 0 if scalar @names < 1;
    if (scalar(@names) < 1) {
	undef $aln;
	return $aln;
    }

    # now got this as a name - sequence hash. Let's make some sequences!

    for $name ( @names ) {
	if( $name =~ m{(\S+)/(\d+)-(\d+)} ) {
	    $seqname = $1;
	    $start = $2;
	    $end = $3;
	} else {
	    $seqname = $name;
	    $start = 1;
	    $str = $hash{$name};
	    $str =~ s/[^0-9A-Za-z$Bio::LocatableSeq::OTHER_SYMBOLS]//g;

	    $end = length($str);
	}

	$seq = Bio::LocatableSeq->new('-seq'        => $hash{$name},
				      '-display_id' => $seqname,
				      '-start'      => $start,
				      '-end'        => $end,
				      '-alphabet'   => $self->alphabet,
				      );
	$aln->add_seq($seq);

#  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;

}

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->num_sequences, $type, $date));

    my $seqCountFormat = "%".($maxname > 20 ? $maxname + 2: 22)."s%-27d%27d\n";
    my $seqNameFormat  = "%-".($maxname > 20 ? $maxname : 20)."s  ";
        
		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!
			$self->_print (sprintf($seqCountFormat,' ',$count+1,$count+50));
			foreach $name  ( @arr ) {
				$self->_print (sprintf($seqNameFormat,$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;

}

General documentation

Please direct usage questions or support issues to the mailing list:
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.

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/

Email: schattner@alum.mit.edu

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _