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.\" ========================================================================
.\"
.IX Title "Bio::FeatureIO::vecscreen_simple 3pm"
.TH Bio::FeatureIO::vecscreen_simple 3pm "2020-01-13" "perl v5.30.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::FeatureIO::vecscreen_simple \- read/write features from NCBI vecscreen \-f 3
output
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 7
\&    # read features 
\&    my $fin = Bio::FeatureIO\->new(\-file=>\*(Aqvecscreen.out\*(Aq,
\&                                  \-format=>\*(Aqvecscreen_simple\*(Aq);
\&    my @vec_regions;
\&    while (my $f = $fin\->next_feature) {
\&      push @vec_regions, $f;
\&    }
\&    
\&    # write features NOT IMPLEMENTED
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
vecscreen is a system for quickly identifying segments of a nucleic
acid sequence that may be of vector origin.  \s-1NCBI\s0 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.
.PP
This module provides parsing for vecscreen '\-f 3' output, described in
the vecscreen documentation as 'Text list, no alignments'
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\& bioperl\-l@bioperl.org                  \- General discussion
\& http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\& http://bugzilla.open\-bio.org/
.Ve
.SH "AUTHOR \- Robert Buels"
.IX Header "AUTHOR - Robert Buels"
Email rmb32 \s-1AT\s0 cornell.edu
.SH "CONTRIBUTORS"
.IX Header "CONTRIBUTORS"
Based on ptt.pm by Torsten Seeman
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "_initialize"
.IX Subsection "_initialize"
Title   : _initialize
Function: Reading? parses the header of the input
          Writing?
.SS "next_feature"
.IX Subsection "next_feature"
.Vb 5
\&  Title   : next_feature
\&  Usage   : $io\->next_feature()
\&  Function: read the next feature from the vecscreen output file
\&  Args    : none
\&  Returns : Bio::SeqFeatureI object
.Ve
.SS "write_feature (\s-1NOT IMPLEMENTED\s0)"
.IX Subsection "write_feature (NOT IMPLEMENTED)"
.Vb 6
\&  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 :
.Ve