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|
=pod
=head1 NAME
Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3
output
=head1 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
=head1 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'
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR - Robert Buels
Email rmb32 AT cornell.edu
=head1 CONTRIBUTORS
Based on ptt.pm by Torsten Seeman
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::FeatureIO::vecscreen_simple;
BEGIN {
$Bio::FeatureIO::vecscreen_simple::AUTHORITY = 'cpan:BIOPERLML';
}
$Bio::FeatureIO::vecscreen_simple::VERSION = '1.6.905';
use strict;
use base qw(Bio::FeatureIO);
use Bio::SeqFeature::Generic;
=head2 _initialize
Title : _initialize
Function: Reading? parses the header of the input
Writing?
=cut
sub _initialize {
my($self,%arg) = @_;
$self->SUPER::_initialize(%arg);
if ($self->mode eq 'r') {
$self->{parse_state}->{seqname} = '';
$self->{parse_state}->{matchtype} = '';
}
else {
$self->throw('vecscreen_simple feature writing not implemented');
}
}
=head2 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
=cut
sub next_feature {
my $self = shift;
return unless $self->mode eq 'r'; # returns if can't read next_feature when we're in write mode
while ( my $line = $self->_readline() ) {
chomp $line;
if ( $line =~ /^>Vector (\S+)/ ) {
$self->{parse_state}{seqname} = $1;
} elsif ( $line =~ /^\s*WARNING/ ) {
$self->warn("$self->{parse_state}{seqname}: vecscreen says: $line\n");
} elsif ( $line =~ /\S/ ) {
$self->{parse_state}{seqname}
or $self->throw("Unexpected line in vecscreen output '$line'");
#if it's not a vector line, it should be either a match type or
#a coordinates line
my $lcline = lc $line;
if ( $line =~ /^(\d+)\s+(\d+)\s*$/ ) {
my ($s,$e) = ($1,$2);
my $matchtype = $self->{parse_state}{matchtype};
$matchtype =~ s/\s/_/g; #replace whitespace with underscores for the primary tag
return Bio::SeqFeature::Generic->new( -start => $s,
-end => $e,
-primary => $matchtype,
-seq_id => $self->{parse_state}{seqname},
);
} elsif ( $lcline eq 'no hits found' ) {
$self->{parse_state}{seqname} = '';
} elsif ( grep $lcline eq $_, 'strong match', 'moderate match', 'weak match', 'suspect origin') {
$self->{parse_state}{matchtype} = $lcline;
} else {
$self->throw("Parse error. Expected a match type or coordinate line but got '$line'");
}
} else {
#blank line, ignore it and reset parser
$self->{parse_state}{seqname} = ''; #< a line with whitespace
#indicates a boundary
#between output for
#different sequences
$self->{parse_state}{matchtype} = '';
}
}
return;
}
=head2 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 :
=cut
sub write_feature {
shift->throw_not_implemented;
}
###
1;#do not remove
###
|
