Login or Register to Ask a Question and Join Our Community

Linux and UNIX Man Pages

Linux & Unix Commands - Search Man Pages

bio::tools::eutilities::query::globalquery(3pm) [debian man page]

Bio::Tools::EUtilities::Query::GlobalQuery(3pm) 	User Contributed Perl Documentation	   Bio::Tools::EUtilities::Query::GlobalQuery(3pm)

NAME

       Bio::Tools::EUtilities::Query::GlobalQuery - container class for egquery data

SYNOPSIS

	 #### should not create instance directly; Bio::Tools::EUtilities does this ####

	 my $parser = Bio::Tools::EUtilities->new(-eutil => 'egquery',
						  -term  => 'BRCA1');

	 # $gquery is a Bio::Tools::EUtilities::Query::GlobalQuery
	 while (my $gquery = $parser->next_GlobalQuery) {
	    print $gquery->to_string."
"; # stringify
	    print "DB:".$gquery->get_db."	".$gquery->get_count;
	 }

DESCRIPTION

       This is a simple container class for egquery data.  Currently this just contains various accessors for the data, such as get_database(),
       get_count(), etc. for each item in a global query.

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@lists.open-bio.org		    - General discussion
	 http://www.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

       Email cjfields at bioperl dot org

APPENDIX

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

   get_term
	Title	: get_term
	Usage	: $st = $qd->get_term;
	Function: retrieve the term for the global search
	Returns : string
	Args	: none

   get_database
	Title	: get_database
	Usage	: $ct = $qd->get_database;
	Function: retrieve the database
	Returns : string
	Args	: none

   get_count
	Title	: get_count
	Usage	: $ct = $qd->get_count;
	Function: retrieve the count for the database
	Returns : string
	Args	: none

   get_status
	Title	: get_status
	Usage	: $st = $qd->get_status;
	Function: retrieve the query status for database in db()
	Returns : string
	Args	: none

   get_menu_name
	Title	: get_menu_name
	Usage	: $ct = $qd->get_menu_name;
	Function: retrieve the full name for the database in db()
	Returns : string
	Args	: None

   to_string
	Title	 : to_string
	Usage	 : $foo->to_string()
	Function : converts current object to string
	Returns  : none
	Args	 : (optional) simple data for text formatting
	Note	 : Used generally for debugging and for the print_GlobalQuery method

perl v5.14.2							    2012-03-02			   Bio::Tools::EUtilities::Query::GlobalQuery(3pm)

Check Out this Related Man Page

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

NAME

       Bio::Tools::RepeatMasker - a parser for RepeatMasker output

SYNOPSIS

	   use Bio::Tools::RepeatMasker;
	   my $parser = Bio::Tools::RepeatMasker->new(-file => 'seq.fa.out');
	   while( my $result = $parser->next_result ) {
	     # get some value
	   }

DESCRIPTION

       A parser for RepeatMasker output

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 - Shawn Hoon
       Email shawnh@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::RepeatMasker->new();
	Function: Builds a new Bio::Tools::RepeatMasker object
	Returns : Bio::Tools::RepeatMasker
	Args	: -fh/-file => $val, for initing input, see Bio::Root::IO

   next_result
	Title	: next_result
	Usage	: my $r = $rpt_masker->next_result
	Function: Get the next result set from parser data
	Returns : Bio::SeqFeature::FeaturePair
		  Feature1 is the Query coordinates and Feature2 is the Hit
	Args	: none

perl v5.14.2							    2012-03-02					     Bio::Tools::RepeatMasker(3pm)
Man Page