Bio::Tools::EMBOSS Palindrome
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Summary
Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output
Package variables
No package variables defined.
Included modules
Bio::SeqFeature::FeaturePair
Bio::SeqFeature::Generic
Inherit
Bio::Root::IO
Synopsis
  # a simple script to turn palindrome output into GFF3
use Bio::Tools::EMBOSS::Palindrome;
use Bio::Tools::GFF;
my $parser = Bio::Tools::EMBOSS::Palindrome->new(-file => $filename); my $out = Bio::Tools::GFF->new(-gff_version => 3, -file => ">$filename.gff"); while( my $seq = $parser->next_seq ) { for my $feat ( $seq->get_SeqFeatures ) { $out->write_feature($feat); } }
Description
This is a parser for the EMBOSS tool 'palindrome'. It will produce a
Bio::Seq object for each sequence analyzed. The sequence will be
empty (but will be of the correct length) and will have attached to it
Bio::SeqFeature::FeaturePair objects which wil It may be consolidated into another framework at a later time, but for
the time being it will stay a separate modules.
Methods
next_seqDescriptionCode
source_tagDescriptionCode
Methods description
next_seqcode    nextTop
 Title   : next_seq
Usage : my $seq = $parser->next_seq;
Function: Get the next feature set from the
Returns : Bio::SeqI object
Args : none
source_tagcodeprevnextTop
 Title   : source_tag
Usage : $obj->source_tag($newval)
Function: Get/Set Source Tag ('palindrome') by default
Returns : value of source_tag (a scalar)
Args : on set, new value (a scalar or undef, optional)
Methods code
next_seqdescriptionprevnextTop
sub next_seq {
    my ($self) = @_;
    my (%searching, $seq,$state);
    my $source = $self->source_tag;
    $state = 0;
    while(defined($_ = $self->_readline)) {
	if( /^\s+$/ ) {
	    next;
	} elsif( /^Palindromes\s+of\s*:\s+(\S+)/o ) {
	    $state = 0;
	    if( $seq )  {
		$self->_pushback($_);
		return $seq;
	    } 
	    $seq = Bio::Seq->new(-display_id => $1);
	    # now get ready to store for the next record
$searching{'-seq_id'} = $1; } elsif( /^Sequence\s+length\s+is\s*:\s+(\d+)/o ) { $seq->length($1); $searching{'-tag'}->{'seqlength'} = $1; } elsif( /^(Start|End)\s+at\s+position\s*:\s+(\d+)/ ) { $searching{'-tag'}->{lc($1)} = $2; } elsif( m/^(Maximum|Minimum)\s+length\s+of\s+Palindromes\s+
is\s*:\s+(\d+)/ox) {
$searching{'-tag'}->{lc($1).'_length'} = $2;
} elsif( /^(Maximum\s+gap)\s+between\s+elements\s+is\s*:\s+(\d+)/o ) { $searching{'-tag'}->{lc($1)} = $2; } elsif( m/^Number\s+of\s+mismatches\s+allowed\s+
in\s+Palindrome\s*:\s+(\d+)/ox ) {
$searching{'-tag'}->{'allowed_mismatches'} = $1;
} elsif( /^Palindromes:/o ) { $state = 1; } elsif( $state == 1 ) { my $feature = Bio::SeqFeature::FeaturePair->new (-primary_tag => 'similarity', -source_tag => $source); for(my $i = 0; $i < 3; $i++ ) { if ($i != 1) { if( /^(\d+)\s+(\S+)\s+(\d+)/o ) { my ($start,$match,$end) = ($1,$2,$3); my $type = $i == 0 ? 'feature1' : 'feature2'; ($start,$end) = sort { $a <=> $b } ($start,$end); $feature->$type( Bio::SeqFeature::Generic->new (%searching, -start => $start, -end => $end, -strand => $i == 0 ? 1 : -1, -primary_tag => 'similarity', -source_tag => $source) ); } else { chomp; warn("Out of sync, line did not match:'$_'\n"); } } $_ = $self->_readline; } $seq->add_SeqFeature($feature); } } return $seq;
}
source_tagdescriptionprevnextTop
sub source_tag {
    my $self = shift;

    return $self->{'source_tag'} = shift if @_;
    return $self->{'source_tag'} || $DEFAULT_SOURCETAG;
}

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
the Bioperl mailing list. 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
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 Title   : new
Usage : my $obj = Bio::Tools::EMBOSS::Palindrome->new();
Function: Builds a new Bio::Tools::EMBOSS::Palindrome object
Returns : an instance of Bio::Tools::EMBOSS::Palindrome
Args : -file/-fh => a filename or filehandle for
initializing the parser