Bio::AlignIO proda
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Summary
Bio::AlignIO::proda - proda sequence input/output stream
This provides the basic capabilities to parse the output alignments
from the ProDA multiple sequence alignment program
(http://proda.stanford.edu)
Package variables
No package variables defined.
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 proda
files.
Methods
_initialize
No description
Code
next_alnDescriptionCode
write_alnDescriptionCode
percentagesDescriptionCode
line_lengthDescriptionCode
no_headerDescriptionCode
Methods description
next_alncode    nextTop
 Title   : next_aln
 Usage   : $aln = $stream->next_aln()
 Function: returns the next alignment in the stream
 Returns : Bio::Align::AlignI object
 Args    : NONE
See Bio::Align::AlignI for details
write_alncodeprevnextTop
 Title   : write_aln
 Usage   : $stream->write_aln(@aln)
 Function: writes the proda-format object (.aln) into the stream
 Returns : 1 for success and 0 for error
 Args    : Bio::Align::AlignI object
percentagescodeprevnextTop
 Title   : percentages
 Usage   : $obj->percentages($newval)
 Function: Set the percentages flag - whether or not to show percentages in
           each output line
 Returns : value of percentages
 Args    : newvalue (optional)
line_lengthcodeprevnextTop
 Title   : line_length
 Usage   : $obj->line_length($newval)
 Function: Set the alignment output line length
 Returns : value of line_length
 Args    : newvalue (optional)
no_headercodeprevnextTop
 Title   : no_header
 Usage   : $obj->no_header($newval)
 Function: Set if the alignment input has a CLUSTAL header or not
 Returns : value of no_header
 Args    : newvalue (optional)
Methods code
_initializedescriptionprevnextTop
sub _initialize {
    my ( $self, @args ) = @_;
    $self->SUPER::_initialize(@args);
    my ( $percentages, $ll ) =
      $self->_rearrange( [qw(PERCENTAGES LINELENGTH)], @args );
    defined $percentages && $self->percentages($percentages);
    $self->line_length( $ll || $LINELENGTH );
}
next_alndescriptionprevnextTop
sub next_aln {
    my ($self) = @_;
    my $first_line;

    while ( $first_line = $self->_readline ) {
        last if $first_line !~ /^$/;
    }
    $self->_pushback($first_line);
    if ( defined( $first_line = $self->_readline )
        && $first_line !~ /\(/ )
    {
        $self->throw(
            "trying to parse a file which does not start with proda headers"
        );
    } else {
        # use it inside the loop
        $self->_pushback($first_line);
    }
    my %alignments;
    my $aln = Bio::SimpleAlign->new(
        -source  => 'proda',
        -verbose => $self->verbose
    );
    my $order = 0;
    my %order;
    $self->{_lastline} = '';
    my ($first_block, $seen_block, $seen_header) = (0,0,0);
    my @ids; my @ids_copy;
    while ( defined( $_ = $self->_readline ) ) {
        next if (/^\s+$/ && !$first_block);
        if (/^\s$/) {  # line contains no description
            $seen_block = 1;
            next;
        }
        $first_block = 1;

        # break the loop if we come to the end of the current alignment
        # and push back the proda header
        if (/\(/ && $seen_header) {
            $self->_pushback($_);
            last;
        }

        if (/\(/ && !$seen_header) {
            @ids = split(' ', $_);
            $seen_header = 1;
            next;
        }

        my ( $seqname, $aln_line ) = ( '', '' );
        if (/^\s*(\S+)\s*\/\s*(\d+)-(\d+)\s+(\S+)\s*$/ox) {

            # clustal 1.4 format
            ( $seqname, $aln_line ) = ( "$1:$2-$3", $4 );

            # } elsif( /^\s*(\S+)\s+(\S+)\s*$/ox ) { without trailing numbers
        }
        elsif (/^\s*(\S+)\s+(\S+)\s*\d*\s*$/ox) {    # with numbers
            ( $seqname, $aln_line ) = ( $1, $2 );
            if ( $seqname =~ /^[\*\.\+\:]+$/ ) {
                $self->{_lastline} = $_;
                next;
            }
        }
        else {
            $self->{_lastline} = $_;
            next;
        }

        # we ended up the first block and now are on the second
        @ids_copy = @ids unless(defined($ids_copy[0])); #FIXME - hacky
        my $seqname_with_coords = shift(@ids_copy);
        if ($seqname_with_coords !~ /$seqname/) {
            {
                $self->throw("header and body of the alignment dont match");
            }
        }
        $alignments{$seqname_with_coords} .= $aln_line;

        if ( !$seen_block ) {
            if (exists $order{$seqname_with_coords}) {
                $self->warn("Duplicate sequence : $seqname\n".
                            "Can't guarantee alignment quality");
            }
            else {
                $order{$seqname_with_coords} = $order++;
            }
        }

    }

    my ( $sname, $start, $end );
    foreach my $name ( sort { $order{$a} <=> $order{$b} } keys %alignments ) {
        if ( $name =~ /(\S+):(\d+)-(\d+)/ ) {
            ( $sname, $start, $end ) = ( $1, $2, $3 );
        }
        else {
            ( $sname, $start ) = ( $name, 1 );
            my $str = $alignments{$name};
            $str =~ s/[^A-Za-z]//g;
            $end = length($str);
        }
        my $seq = Bio::LocatableSeq->new(
					 -seq      => $alignments{$name},
					 -id       => $sname,
					 -start    => $start,
					 -end      => $end,
					 -alphabet => $self->alphabet,
					 );
        $aln->add_seq($seq);
    }
    
    return $aln if $aln->num_sequences;
    return;
}
write_alndescriptionprevnextTop
sub write_aln {
    my ($self,@aln) = @_;
    $self->throw_not_implemented();
}
percentagesdescriptionprevnextTop
sub percentages {
    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_percentages'} = $value;
    }
    return $self->{'_percentages'};
}
line_lengthdescriptionprevnextTop
sub line_length {
    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_line_length'} = $value;
    }
    return $self->{'_line_length'};
}
no_headerdescriptionprevnextTop
sub no_header {
    my ( $self, $value ) = @_;
    if ( defined $value ) {
        $self->{'_no_header'} = $value;
    }
    return $self->{'_no_header'};
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
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 - Albert VilellaTop
Email: avilella-at-gmail-dot-com
APPENDIXTop
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
newTop
 Title   : new
 Usage   : $alignio = Bio::AlignIO->new(-format => 'proda',
                       -file => 'filename');
 Function: returns a new Bio::AlignIO object to handle proda files
 Returns : Bio::AlignIO::proda object
 Args    : -verbose => verbosity setting (-1, 0, 1, 2)
           -file    => name of file to read in or to write, with ">"
           -fh      => alternative to -file param - provide a filehandle
                       to read from or write to
           -format  => alignment format to process or produce
           -percentages => display a percentage of identity
                           in each line of the alignment (proda only)
           -linelength=> alignment output line length (default 60)