Bio::Tools::isPcr(3)

NAME
Bio::Tools::isPcr - Parse isPcr output and make features

SYNOPSIS
    # A simple annotation pipeline wrapper for isPcr data
    # assuming isPcr data is already generated in file seq1.isPcr
    # and sequence data is in fasta format in file called seq1.fa

    # Note: this parser is meant for the default fasta output from
    # isPcr.  bed and psl output formats are not supported.

    use Bio::Tools::IsPcr;
    use Bio::SeqIO;
    my $parser = Bio::Tools::isPcr->new(-file => 'seq1.isPcr');
    my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => 'seq1.fa');
    my $seq = $seqio->next_seq || die("cannot get a seq object from SeqIO");

    while( my $feat = $parser->next_feature ) {
        # add isPcr annotation to a sequence
        $seq->add_SeqFeature($feat);
    }
    my $seqout = Bio::SeqIO->new(-format => 'embl');
    $seqout->write_seq($seq);

DESCRIPTION
This object serves as a parser for isPcr data (in the default fasta format), creating a Bio::SeqFeatureI for each isPcr hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation.

This module is adapted from the Bio::Tools::EPCR module written by Jason Stajich (jason-at-bioperl.org).

FEEDBACK

  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

  Support
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.

  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/

AUTHOR - Sheldon McKay
Email mckays@cshl.edu

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  new
 Title   : new
 Usage   : my $ispcr = Bio::Tools::isPcr->new( -file => $file,
                                              -primary => $fprimary,
                                              -source => $fsource,
                                              -groupclass => $fgroupclass);

 Function: Initializes a new isPcr parser
 Returns : Bio::Tools::isPcr
 Args    : -fh   => filehandle
           OR
           -file => filename

           -primary => a string to be used as the common value for
                       each features '-primary' tag.  Defaults to
                       the sequence ontology term 'PCR_product'.
                       (This in turn maps to the GFF 'type'
                       tag (aka 'method')).

            -source => a string to be used as the common value for
                       each features '-source' tag.  Defaults to
                       'isPcr'. (This in turn maps to the GFF 'source'
                       tag)

            -groupclass => a string to be used as the name of the tag
                           which will hold the sts marker namefirst
                           attribute.  Defaults to 'name'.

  next_feature
 Title   : next_feature
 Usage   : $seqfeature = $obj->next_feature();
 Function: Returns the next feature available in the analysis result, or
           undef if there are no more features.
 Example :
 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
           more features.
 Args    : none

  source
 Title   : source
 Usage   : $obj->source($newval)
 Function:
 Example :
 Returns : value of source (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

  primary
 Title   : primary
 Usage   : $obj->primary($newval)
 Function:
 Example :
 Returns : value of primary (a scalar)
 Args    : on set, new value (a scalar or undef, optional)

  groupclass
 Title   : groupclass
 Usage   : $obj->groupclass($newval)
 Function:
 Example :
 Returns : value of groupclass (a scalar)
 Args    : on set, new value (a scalar or undef, optional)