| Bio::Tools::Run::Promoterwise(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Promoterwise(3pm) |
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 mailing lists. Your participation is much appreciated.
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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.
Report bugs to the Bioperl bug tracking system to help us keep
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http://redmine.open-bio.org/projects/bioperl/
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 :
| 2018-09-14 | perl v5.26.2 |