Bio::Tools::Run::Promoterwise man page on Fedora

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Bio::Tools::Run::PromoUseriContributed Perl DoBio::Tools::Run::Promoterwise(3)

NAME
       Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences
       using promoterwise

SYNOPSIS
	 # Build a Promoterwise alignment factory
	 my @params = ('-s'=>1,'-query_start'=>10,'-dymem'=>1);
	 my  $factory = Bio::Tools::Run::Promoterwise->new(@params);

	 my (@fp)= $factory->run($seq1,$seq2);

	 # each feature pair is a group of hsps
	 foreach my $fp(@fp){
	   print "Hit Length: ".$fp->feature1->length."\n";
	   print "Hit Start: ".$fp->feature1->start."\n";
	   print "Hit End: ".$fp->feature1->end."\n";
	   print "Hsps: \n";
	   my @first_hsp = $fp->feature1->sub_SeqFeature;
	   my @second_hsp = $fp->feature2->sub_SeqFeature;
	   for ($i..$#first_hsp){
	     print $first_hsp[$i]->seq." ".$second_hsp[$i]->seq."\n";
	   }
	 }
	 print "end: ". $fp->feature2->start."\t".$fp->feature2->end."\n";

	 #Available parameters include:
	 #( S T U V QUERY_START QUERY_END TARGET_START
	 #TARGET_END LHWINDOW LHSEED LHALN LHSCORE LHREJECT
	 #LHREJECT LHMAX DYMEM KBYTE DYCACHE)
	 #For an explanation of these parameters, please see documentation
	 #from the Wise package.

DESCRIPTION
       Promoterwise is an alignment algorithm that relaxes the constraint that
       local alignments have to be co-linear. Otherwise it provides a similar
       model to DBA, which is designed for promoter sequence alignments by
       Ewan Birney.  It is part of the wise2 package available at:
       http://www.sanger.ac.uk/software/wise2.

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:

	 http://bugzilla.open-bio.org/

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 _

   program_name
	Title	: program_name
	Usage	: $factory>program_name()
	Function: holds the program name
	Returns:  string
	Args	: None

   program_dir
	Title	: program_dir
	Usage	: $factory->program_dir(@params)
	Function: returns the program directory, obtained from ENV variable.
	Returns:  string
	Args	:

   version
	Title	: version
	Usage	: exit if $prog->version() < 1.8
	Function: Determine the version number of the program
	Example :
	Returns : float or undef
	Args	: none

   run
	Title	: run
	Usage	: 2 sequence objects
		  @fp = $factory->run($seq1, $seq2);
	Function: run
	Returns : An array of <Bio::SeqFeature::FeaturePair>
	Args	: Name of a file containing a set of 2 fasta sequences
		  or else 2  Bio::Seq objects.

       Throws an exception if argument is not either a string (eg a filename)
       or 2 Bio::Seq objects.  If arguments are strings, throws exception if
       file corresponding to string name can not be found.

   _run
	Title	:  _run
	Usage	:  Internal function, not to be called directly
	Function:   makes actual system call to a promoterwise program
	Example :
	Returns : L<Bio::SeqFeature::FeaturePair>
	Args	: Name of a files containing 2 sequences in the order of peptide and genomic

   _setparams
	Title	:  _setparams
	Usage	:  Internal function, not to be called directly
	Function:  creates a string of params to be used in the command string
	Example :
	Returns :  string of params
	Args	:

   _query_pep_seq
	Title	:  _query_pep_seq
	Usage	:  Internal function, not to be called directly
	Function:  get/set for the query sequence
	Example :
	Returns :
	Args	:

   _subject_dna_seq
	Title	:  _subject_dna_seq
	Usage	:  Internal function, not to be called directly
	Function:  get/set for the subject sequence
	Example :
	Returns :

	Args	:

perl v5.14.1			  2011-07-21  Bio::Tools::Run::Promoterwise(3)
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