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Summary

Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3
output

Package variables

Included modules

Inherit

Bio::FeatureIO

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'

Methods

Methods description

  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 :

Methods code

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');
 }

}

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;

}

sub write_feature {

 shift->throw_not_implemented;
}


###
1;#do not remove
###

}

General documentation

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

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:

 https://redmine.open-bio.org/projects/bioperl/

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 _