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.\"
.IX Title "Bio::Tools::Run::Promoterwise 3pm"
.TH Bio::Tools::Run::Promoterwise 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Promoterwise \- Wrapper for aligning two sequences using
promoterwise
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  # Build a Promoterwise alignment factory
\&  my @params = (\*(Aq\-s\*(Aq=>1,\*(Aq\-query_start\*(Aq=>10,\*(Aq\-dymem\*(Aq=>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."\en";
\&    print "Hit Start: ".$fp\->feature1\->start."\en";
\&    print "Hit End: ".$fp\->feature1\->end."\en";
\&    print "Hsps: \en";
\&    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."\en";
\&    }
\&  }
\&  print "end: ". $fp\->feature2\->start."\et".$fp\->feature2\->end."\en";
\&
\&  #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.
.Ve
.SH "DESCRIPTION"
.IX Header "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 \s-1DBA,\s0 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.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Shawn Hoon"
.IX Header "AUTHOR - Shawn Hoon"
Email: shawnh@fugu\-sg.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $factory>program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $factory\->program_dir(@params)
\& Function: returns the program directory, obtained from ENV variable.
\& Returns:  string
\& Args    :
.Ve
.SS "version"
.IX Subsection "version"
.Vb 6
\& Title   : version
\& Usage   : exit if $prog\->version() < 1.8
\& Function: Determine the version number of the program
\& Example :
\& Returns : float or undef
\& Args    : none
.Ve
.SS "run"
.IX Subsection "run"
.Vb 7
\& 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.
.Ve
.PP
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.
.SS "_run"
.IX Subsection "_run"
.Vb 6
\& 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
.Ve
.SS "_setparams"
.IX Subsection "_setparams"
.Vb 6
\& 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    :
.Ve
.SS "_query_pep_seq"
.IX Subsection "_query_pep_seq"
.Vb 6
\& Title   :  _query_pep_seq
\& Usage   :  Internal function, not to be called directly
\& Function:  get/set for the query sequence
\& Example :
\& Returns :  
\& Args    :
.Ve
.SS "_subject_dna_seq"
.IX Subsection "_subject_dna_seq"
.Vb 5
\& Title   :  _subject_dna_seq
\& Usage   :  Internal function, not to be called directly
\& Function:  get/set for the subject sequence
\& Example :
\& Returns :
\&
\& Args    :
.Ve