Bio::Tools::EPCR man page on Fedora

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Bio::Tools::EPCR(3)   User Contributed Perl Documentation  Bio::Tools::EPCR(3)

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)

perl v5.14.1			  2011-07-22		   Bio::Tools::EPCR(3)
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