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

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NAME

Bio::Tools::EPCR - Parse ePCR output and make features

CONTENTS

SYNOPSIS



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

    use Bio::Tools::EPCR;
    use Bio::SeqIO;
    my $parser = Bio::Tools::EPCR->new(-file => seq1.epcr);
    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 EPCR 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 ePCR data, creating a Bio::SeqFeatureI for each ePCR hit. These can be processed or added as annotation to an existing Bio::SeqI object for the purposes of automated annotation.

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 - Jason Stajich

Email jason-at-bioperl.org

APPENDIX

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

    new



 Title   : new
 Usage   : my $epcr = Bio::Tools::EPCR->new(-file => $file,
                                           -primary => $fprimary,
                                           -source => $fsource,
                                           -groupclass => $fgroupclass);
 Function: Initializes a new EPCR parser
 Returns : Bio::Tools::EPCR
 Args    : -fh   => filehandle
           OR
           -file => filename

           -primary => a string to be used as the common value for
                       each features -primary tag.  Defaults to
                       sts.  (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
                       e-PCR. (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::EPCR (3) 2016-04-05

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