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Bio::Tools::EMBOSS::Palindrome.3pm
Langue: en
Version: 2009-03-10 (debian - 07/07/09)
Section: 3 (Bibliothèques de fonctions)
Sommaire
NAME
Bio::Tools::EMBOSS::Palindrome - parse EMBOSS palindrome outputSYNOPSIS
# 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 wilFUTURE WORK
It may be consolidated into another framework at a later time, but for the time being it will stay a separate modules.FEEDBACK
Mailing Lists
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
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.open-bio.org/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-orgAPPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _new
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
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)
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