++ed by:
PROCH DEMIAN YUSRIDEB THALJEF GENEHACK

11 PAUSE users
14 non-PAUSE users.

Christopher Fields
and 1 contributors

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

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 :