bio::tools::seg(3pm) [debian man page]

Bio::Tools::Seg(3pm)					User Contributed Perl Documentation				      Bio::Tools::Seg(3pm)

NAME

       Bio::Tools::Seg - parse "seg" output

SYNOPSIS

	 use Bio::Tools::Seg;
	 my $parser = Bio::Tools::Seg->(-file => 'seg.fasta');
	 while ( my $f = $parser->next_result ) {
	   if ($f->score < 1.5) {
	     print $f->location->to_FTstring, " is low complexity
";
	   }
	 }

DESCRIPTION

       "seg" identifies low-complexity regions on a protein sequence.  It is usually part of the "WU-BLAST" and "InterProScan" packages.

       The Bio::Tools::Seg module will only parse the "fasta" output modes of "seg", i.e. "seg -l" (low complexity regions only), "seg -h" (high
       complexity regions only), or "seg -a" (both low and high).

       It creates a Bio::SeqFeature::Generic for each FASTA-like entry found in the input file. It is up to the user to appropriately filter these
       using the feature's score.

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 - Torsten Seemann
       Email - torsten.seemann AT infotech.monash.edu.au

CONTRIBUTOR - Bala
       Email - savikalpa@fugu-sg.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 $obj = Bio::Tools::Seg->new();
	Function: Builds a new Bio::Tools::Seg object
	Returns : Bio::Tools::Seg
	Args	: -fh/-file => $val, # for initing input, see Bio::Root::IO

   next_result
	Title	: next_result
	Usage	: my $feat = $seg->next_result
	Function: Get the next result set from parser data
	Returns : Bio::SeqFeature::Generic
	Args	: none

perl v5.14.2							    2012-03-02						      Bio::Tools::Seg(3pm)

Check Out this Related Man Page

Bio::Tools::Hmmpfam(3pm)				User Contributed Perl Documentation				  Bio::Tools::Hmmpfam(3pm)

NAME

       Bio::Tools::Hmmpfam - Parser for Hmmpfam program

SYNOPSIS

	 use Bio::Tools::Hmmpfam;
	 my @hmmpfam_feat;
	 my $hmmpfam_parser = Bio::Tools::Hmmpfam->new(-fh =>$filehandle );
	 while( my $hmmpfam_feat = $hmmpfam_parser->next_result ) {
	       push @hmmpfam_feat, $hmmpfam_feat;
	 }

DESCRIPTION

       Parser for Hmmpfam  program.  See also Bio::SearchIO::hmmer.

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 - Balamurugan Kumarasamy
	Email: fugui@worf.fugu-sg.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 $obj = Bio::Tools::Hmmpfam->new(-fh=>$filehandle);
	Function: Builds a new Bio::Tools::Hmmpfam object
	Returns : Bio::Tools::Hmmpfam
	Args	: -filename
		  -fh (filehandle)

   next_result
	Title	: next_result
	Usage	: my $feat = $hmmpfam_parser->next_result
	Function: Get the next result set from parser data
	Returns : L<Bio::SeqFeature::Generic>
	Args	: none

   create_feature
	Title	: create_feature
	Usage	: my $feat=$hmmpfam_parser->create_feature($feature,$seqname)
	Function: creates a SeqFeature Generic object
	Returns : L<Bio::SeqFeature::Generic>
	Args	:

   seqname
	Title	:   seqname
	Usage	:   obj->seqname($seqname)
	Function:   Internal(not to be used directly)
	Returns :
	Args	:   seqname

perl v5.14.2							    2012-03-02						  Bio::Tools::Hmmpfam(3pm)

Linux and UNIX Man Pages

bio::tools::seg(3pm) [debian man page]

Check Out this Related Man Page