Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3
output
# 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
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'
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
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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.
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/
Email rmb32 AT cornell.edu
Based on ptt.pm by Torsten Seeman
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : _initialize Function: Reading? parses the header of the input
Writing?
Title : next_feature
Usage : $io->next_feature()
Function: read the next feature from the vecscreen output file
Args : none
Returns : Bio::SeqFeatureI object
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 :