Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome output # 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); } } 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

FUTURE WORK
It may be consolidated into another framework at a later time, but for the time being it will stay a separate modules.

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Reporting Bugs
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.bioperl.org/ Email jason-at-bioperl-dot-org Describe contact details here Additional contributors names and emails here The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new
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

next_seq
Title : next_seq Usage : my $seq = $parser->next_seq; Function: Get the next feature set from the Returns : L<Bio::SeqI> object Args : none

source_tag
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)