Bio::Tools::EMBOSS
Palindrome
Summary
Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
# a simple script to turn palindrome output into GFF3
use Bio::Tools::EMBOSS::Palindrome;
use Bio::Tools::GFF;
my $parser = new Bio::Tools::EMBOSS::Palindrome(-file => $filename);
my $out = new Bio::Tools::GFF(-gff_version => 3,
-file => ">$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
Methods description
Title : next_seq
Usage : my $seq = $parser->next_seq;
Function: Get the next feature set from the
Returns : Bio::SeqI object
Args : none |
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
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 = new Bio::Seq(-display_id => $1);
$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 = new Bio::SeqFeature::FeaturePair
(-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);} | sub source_tag
{ my $self = shift;
return $self->{'source_tag'} = shift if @_;
return $self->{'source_tag'} || $DEFAULT_SOURCETAG;} | General documentation
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
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:
http://bugzilla.open-bio.org/
| AUTHOR - Jason Stajich | Top |
Email jason-at-bioperl-dot-org
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : new
Usage : my $obj = new Bio::Tools::EMBOSS::Palindrome();
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