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Bio::FeatureIO::vecscreen_simple - read/write features from NCBI vecscreen -f 3
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my $fin = Bio::FeatureIO->new(-file=>'vecscreen.out',
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-format=>'vecscreen_simple');
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while (my $f = $fin->next_feature) {
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push @vec_regions, $f;
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# write features NOT IMPLEMENTED
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vecscreen is a system for quickly identifying segments of a nucleic
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acid sequence that may be of vector origin. NCBI developed vecscreen
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to minimize the incidence and impact of vector contamination in public
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sequence databases. GenBank Annotation Staff use vecscreen to verify
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that sequences submitted for inclusion in the database are free from
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contaminating vector sequence. Any sequence can be screened for vector
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contamination using vecscreen.
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This module provides parsing for vecscreen '-f 3' output, described in
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the vecscreen documentation as 'Text list, no alignments'
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User feedback is an integral part of the evolution of this and other
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Bioperl modules. Send your comments and suggestions preferably to
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the Bioperl mailing list. Your participation is much appreciated.
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bioperl-l@bioperl.org - General discussion
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists
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Please direct usage questions or support issues to the mailing list:
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I<bioperl-l@bioperl.org>
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rather than to the module maintainer directly. Many experienced and
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reponsive experts will be able look at the problem and quickly
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address it. Please include a thorough description of the problem
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with code and data examples if at all possible.
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Report bugs to the Bioperl bug tracking system to help us keep track
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of the bugs and their resolution. Bug reports can be submitted via
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https://redmine.open-bio.org/projects/bioperl/
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=head1 AUTHOR - Robert Buels
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Email rmb32 AT cornell.edu
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Based on ptt.pm by Torsten Seeman
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The rest of the documentation details each of the object methods.
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Internal methods are usually preceded with a _
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# Let the code begin...
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package Bio::FeatureIO::vecscreen_simple;
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use base qw(Bio::FeatureIO);
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use Bio::SeqFeature::Generic;
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Function: Reading? parses the header of the input
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$self->SUPER::_initialize(%arg);
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if ($self->mode eq 'r') {
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$self->{parse_state}->{seqname} = '';
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$self->{parse_state}->{matchtype} = '';
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$self->throw('vecscreen_simple feature writing not implemented');
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Usage : $io->next_feature()
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Function: read the next feature from the vecscreen output file
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Returns : Bio::SeqFeatureI object
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return unless $self->mode eq 'r'; # returns if can't read next_feature when we're in write mode
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while ( my $line = $self->_readline() ) {
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if ( $line =~ /^>Vector (\S+)/ ) {
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$self->{parse_state}{seqname} = $1;
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} elsif ( $line =~ /^\s*WARNING/ ) {
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$self->warn("$self->{parse_state}{seqname}: vecscreen says: $line\n");
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} elsif ( $line =~ /\S/ ) {
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$self->{parse_state}{seqname}
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or $self->throw("Unexpected line in vecscreen output '$line'");
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#if it's not a vector line, it should be either a match type or
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my $lcline = lc $line;
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if ( $line =~ /^(\d+)\s+(\d+)\s*$/ ) {
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my ($s,$e) = ($1,$2);
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my $matchtype = $self->{parse_state}{matchtype};
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$matchtype =~ s/\s/_/g; #replace whitespace with underscores for the primary tag
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return Bio::SeqFeature::Generic->new( -start => $s,
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-primary => $matchtype,
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-seq_id => $self->{parse_state}{seqname},
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} elsif ( $lcline eq 'no hits found' ) {
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$self->{parse_state}{seqname} = '';
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} elsif ( grep $lcline eq $_, 'strong match', 'moderate match', 'weak match', 'suspect origin') {
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$self->{parse_state}{matchtype} = $lcline;
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$self->throw("Parse error. Expected a match type or coordinate line but got '$line'");
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#blank line, ignore it and reset parser
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$self->{parse_state}{seqname} = ''; #< a line with whitespace
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#indicates a boundary
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$self->{parse_state}{matchtype} = '';
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=head2 write_feature (NOT IMPLEMENTED)
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Title : write_feature
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Usage : $io->write_feature($feature)
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Function: write a Bio::SeqFeatureI object in vecscreen -f 3 format
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Args : Bio::SeqFeatureI object
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shift->throw_not_implemented;
added
removed
Bio/FeatureIO/vecscreen_simple.pm
