Bio::Tools::Run::Promoterwise.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

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    :