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Bio::FeatureIO::vecscrUsersContributed PerlBio::FeatureIO::vecscreen_simple(3)

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:

	http://bugzilla.open-bio.org/

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 v5.32.0			  2014-09-0Bio::FeatureIO::vecscreen_simple(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Robert Buels | CONTRIBUTORS | APPENDIX

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