Bio::Tools::isPcr man page on Pidora

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

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 = 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:

	 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 = 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)

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