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Manual Reference Pages  -  BIO::TOOLS::ISPCR (3)

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NAME

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

CONTENTS

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:



  https://github.com/bioperl/bioperl-live/issues



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)



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perl v5.20.3 BIO::TOOLS::ISPCR (3) 2016-04-05

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