debian man page for bio::featureio::vecscreen_simple

Bio::FeatureIO::vecscreen_simple(3pm)			User Contributed Perl Documentation		     Bio::FeatureIO::vecscreen_simple(3pm)

NAME
       Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3 output

SYNOPSIS
	   # read features
	   my $fin = Bio::FeatureIO->new(-file=>'vecscreen.out',
					 -format=>'vecscreen_simple');
	   my @vec_regions;
	   while (my $f = $fin->next_feature) {
	     push @vec_regions, $f;
	   }

	   # write features NOT IMPLEMENTED

DESCRIPTION
       vecscreen is a system for quickly identifying segments of a nucleic acid sequence that may be of vector origin.	NCBI developed vecscreen
       to minimize the incidence and impact of vector contamination in public sequence databases.  GenBank Annotation Staff use vecscreen to
       verify that sequences submitted for inclusion in the database are free from contaminating vector sequence. Any sequence can be screened for
       vector contamination using vecscreen.

       This module provides parsing for vecscreen '-f 3' output, described in the vecscreen documentation as 'Text list, no alignments'

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

   Support
       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 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 the
       web:

	https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Robert Buels
       Email rmb32 AT cornell.edu

CONTRIBUTORS
       Based on ptt.pm by Torsten Seeman

APPENDIX
       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   _initialize
       Title   : _initialize Function: Reading? parses the header of the input
		 Writing?

   next_feature
	 Title	 : next_feature
	 Usage	 : $io->next_feature()
	 Function: read the next feature from the vecscreen output file
	 Args	 : none
	 Returns : Bio::SeqFeatureI object

   write_feature (NOT IMPLEMENTED)
	 Title	 : write_feature
	 Usage	 : $io->write_feature($feature)
	 Function: write a Bio::SeqFeatureI object in vecscreen -f 3 format
	 Example :
	 Args	 : Bio::SeqFeatureI object
	 Returns :

perl v5.14.2							    2012-03-02				     Bio::FeatureIO::vecscreen_simple(3pm)