bio::seqio::fthelper(3pm) [debian man page]

Bio::SeqIO::FTHelper(3pm)				User Contributed Perl Documentation				 Bio::SeqIO::FTHelper(3pm)

NAME

       Bio::SeqIO::FTHelper - Helper class for Embl/Genbank feature tables

SYNOPSIS

       Used by Bio::SeqIO::EMBL,Bio::SeqIO::genbank, and Bio::SeqIO::swiss to help process the Feature Table

DESCRIPTION

       Represents one particular Feature with the following fields

	     key - the key of the feature
	     loc - the location string of the feature
	     <other fields> - other fields

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 one
       of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

CONTRIBUTORS

       Jason Stajich jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   _generic_seqfeature
	Title	: _generic_seqfeature
	Usage	: $fthelper->_generic_seqfeature($annseq, "GenBank")
	Function: processes fthelper into a generic seqfeature
	Returns : TRUE on success and otherwise FALSE
	Args	: The Bio::Factory::LocationFactoryI object to use for parsing
		  location strings. The ID (e.g., display_id) of the sequence on which
		  this feature is located, optionally a string indicating the source
		  (GenBank/EMBL/SwissProt)

   from_SeqFeature
	Title	: from_SeqFeature
	Usage	: @fthelperlist = Bio::SeqIO::FTHelper::from_SeqFeature($sf,
							    $context_annseq);
	Function: constructor of fthelpers from SeqFeatures
		:
		: The additional annseq argument is to allow the building of FTHelper
		: lines relevant to particular sequences (ie, when features are spread over
		: enteries, knowing how to build this)
	Returns : an array of FThelpers
	Args	: seq features

   key
	Title	: key
	Usage	: $obj->key($newval)
	Function:
	Example :
	Returns : value of key
	Args	: newvalue (optional)

   loc
	Title	: loc
	Usage	: $obj->loc($newval)
	Function:
	Example :
	Returns : value of loc
	Args	: newvalue (optional)

   field
	Title	: field
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   add_field
	Title	: add_field
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

perl v5.14.2							    2012-03-02						 Bio::SeqIO::FTHelper(3pm)

Check Out this Related Man Page

Bio::SeqIO::MultiFile(3pm)				User Contributed Perl Documentation				Bio::SeqIO::MultiFile(3pm)

NAME

       Bio::SeqIO::MultiFile - Treating a set of files as a single input stream

SYNOPSIS

	  $seqin = Bio::SeqIO::MultiFile( '-format' => 'Fasta',
					  '-files'  => ['file1','file2'] );
	  while((my $seq = $seqin->next_seq)) {
	      # do something with $seq
	  }

DESCRIPTION

       Bio::SeqIO::MultiFile provides a simple way of bundling a whole set of identically formatted sequence input files as a single stream.

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 one
       of the Bioperl mailing lists.  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 the bugs and their resolution.  Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Ewan Birney
       Email birney@ebi.ac.uk

APPENDIX

       The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

   next_seq
	Title	: next_seq
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   next_primary_seq
	Title	: next_primary_seq
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _load_file
	Title	: _load_file
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _set_file
	Title	: _set_file
	Usage	:
	Function:
	Example :
	Returns :
	Args	:

   _current_seqio
	Title	: _current_seqio
	Usage	: $obj->_current_seqio($newval)
	Function:
	Example :
	Returns : value of _current_seqio
	Args	: newvalue (optional)

   _format
	Title	: _format
	Usage	: $obj->_format($newval)
	Function:
	Example :
	Returns : value of _format
	Args	: newvalue (optional)

perl v5.14.2							    2012-03-02						Bio::SeqIO::MultiFile(3pm)

Linux and UNIX Man Pages

bio::seqio::fthelper(3pm) [debian man page]

Check Out this Related Man Page