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'
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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 :
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.