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Bio::Tools::ipcress(3)User Contributed Perl DocumentatioBio::Tools::ipcress(3)

NAME
       Bio::Tools::ipcress - Parse ipcress output and make features

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

	   use Bio::Tools::ipcress;
	   use Bio::SeqIO;
	   my $parser =	Bio::Tools::ipcress->new(-file => 'seq1.ipcress');
	   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 ipcress 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 ipcress data,	creating a
       Bio::SeqFeatureI	for each ipcress 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).

       Ipcress is available through Guy	Slater's Exonerate package
       http://www.ebi.ac.uk/~guy/exonerate/

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 - 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 $ipcress =	Bio::Tools::ipcress->new(-file => $file,
						  -primary => $fprimary,
						  -source => $fsource,
						  -groupclass => $fgroupclass);
	Function: Initializes a	new ipcress parser
	Returns	: Bio::Tools::ipcress
	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
			      'ipcress'. (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 v5.32.1			  2019-12-07		Bio::Tools::ipcress(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Sheldon McKay | APPENDIX

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