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Bio::FeatureIO::vecscreen_simple(3pm) User Contributed Perl Documentation Bio::FeatureIO::vecscreen_simple(3pm)


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


    # read features 
    my $fin = Bio::FeatureIO->new(-file=>'vecscreen.out',
    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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AUTHOR - Robert Buels

Email rmb32 AT


Based on 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


  Title   : next_feature
  Usage   : $io->next_feature()
  Function: read the next feature from the vecscreen output file
  Args    : none
  Returns : Bio::SeqFeatureI object

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 :
2020-01-13 perl v5.30.0