Bio::AlignIO msf
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Summary
Bio::AlignIO::msf - msf sequence input/output stream
Package variables
No package variables defined.
Included modules
Bio::SeqIO::gcg
Bio::SimpleAlign
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
BEGIN Code
next_alnDescriptionCode
write_alnDescriptionCode
Methods description
next_alncode    nextTop
 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
write_alncodeprevnextTop
 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
BEGINTop
BEGIN {
	%valid_type = qw( dna N rna N protein P );
}
next_alndescriptionprevnextTop
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 $aln->num_sequences; return;
}
write_alndescriptionprevnextTop
sub write_aln {
	my ($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
FEEDBACKTop
Support Top
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.
Reporting BugsTop
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/
AUTHORS - Peter SchattnerTop
Email: schattner@alum.mit.edu
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _