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 = new Bio::Tools::isPcr(-file => 'seq1.isPcr');
    my $seqio = new Bio::SeqIO(-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 = new Bio::SeqIO(-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

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 = new Bio::Tools::isPcr( -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)