Bio::Tools::Run::Promoterwise - Wrapper for aligning two sequences using
promoterwise
# 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.
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.
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
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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.
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Email: shawnh@fugu-sg.org
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
Title : program_name
Usage : $factory>program_name()
Function: holds the program name
Returns: string
Args : None
Title : program_dir
Usage : $factory->program_dir(@params)
Function: returns the program directory, obtained from ENV variable.
Returns: string
Args :
Title : version
Usage : exit if $prog->version() < 1.8
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
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.
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
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 :
Title : _query_pep_seq
Usage : Internal function, not to be called directly
Function: get/set for the query sequence
Example :
Returns :
Args :
Title : _subject_dna_seq
Usage : Internal function, not to be called directly
Function: get/set for the subject sequence
Example :
Returns :
Args :