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)