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

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

NAME

       Bio::SeqIO::interpro - InterProScan XML input/output stream

SYNOPSIS

	 # do not call this module directly, use Bio::SeqIO

	 use strict;
	 use Bio::SeqIO;

	 my $io = Bio::SeqIO->new(-format => "interpro",
				  -file   => $interpro_file);

	 while (my $seq = $io->next_seq) {
	   # use the Sequence object
	 }

DESCRIPTION

       Bio::SeqIO::interpro will parse Interpro scan XML (version 1.2) and create Bio::SeqFeature::Generic objects based on the contents of the
       XML document.

       Bio::SeqIO::interpro will also attach the annotation given in the XML file to the Bio::SeqFeature::Generic objects that it creates.

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

AUTHOR - Jared Fox
       Email jaredfox@ucla.edu

CONTRIBUTORS

       Allen Day allenday@ucla.edu

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	: my $seqobj = $stream->next_seq
	Function: Retrieves the next sequence from a SeqIO::interpro stream.
	Returns : A Bio::Seq::RichSeq object
	Args	:

   _initialize
	Title	: _initialize
	Usage	:
	Function:
	Returns :
	Args	:

   _sequence_factory
	Title	: _sequence_factory
	Usage	:
	Function:
	Returns :
	Args	:

   _xml_parser
	Title	: _xml_parser
	Usage	:
	Function:
	Returns :
	Args	:

   _parse_xml
	Title	: _parse_xml
	Usage	:
	Function:
	Returns :
	Args	:

   _dom
	Title	: _dom
	Usage	:
	Function:
	Returns :
	Args	:

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

Check Out this Related Man Page

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

NAME

       Bio::SeqIO::bsml_sax - BSML sequence input/output stream using SAX

SYNOPSIS

	It is probably best not to use this object directly, but rather go
	through the SeqIO handler system. To read a BSML file:

	   $stream = Bio::SeqIO->new( -file => $filename, -format => 'bsml');

	   while ( my $bioSeqObj = $stream->next_seq() ) {
	       # do something with $bioSeqObj
	   }

	To write a Seq object to the current file handle in BSML XML format:

	   $stream->write_seq( -seq => $seqObj);

	If instead you would like a XML::DOM object containing the BSML, use:

	   my $newXmlObject = $stream->to_bsml( -seq => $seqObj);

DEPENDENCIES

	In addition to parts of the Bio:: hierarchy, this module uses:

	XML::SAX

DESCRIPTION

	This object can transform Bio::Seq objects to and from BSML (XML)
	flatfiles.

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 - Jason Stajich
       Email jason-at-bioperl-dot-org

METHODS

   next_seq
	Title	: next_seq
	Usage	: my $bioSeqObj = $stream->next_seq
	Function: Retrieves the next sequence from a SeqIO::bsml stream.
	Returns : A reference to a Bio::Seq::RichSeq object
	Args	:

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