Bio::Tools::EPCR.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

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

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:
   http://bugzilla.open-bio.org/
 
 

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)