| Bio::Tools::Run::Alignment::Exonerate(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Alignment::Exonerate(3pm) |
Bio::Tools::Run::Alignment::Exonerate
use Bio::Tools::Run::Alignment::Exonerate;
use Bio::SeqIO;
my $qio = Bio::SeqIO->new(-file=>$ARGV[0],-format=>'fasta');
my $query = $qio->next_seq();
my $tio = Bio::SeqIO->new(-file=>$ARGV[1],-format=>'fasta');
my $target = $sio->next_seq();
#exonerate parameters can all be passed via arguments parameter.
#parameters passed are not checked for validity
my $run = Bio::Tools::Run::Alignment::Exonerate->
new(arguments=>'--model est2genome --bestn 10');
my $searchio_obj = $run->run($query,$target);
while(my $result = $searchio->next_result){
while( my $hit = $result->next_hit ) {
while( my $hsp = $hit->next_hsp ) {
print $hsp->start."\t".$hsp->end."\n";
}
}
}
Wrapper for Exonerate alignment program. You can get exonerate at http://www.ebi.ac.uk/~guy/exonerate/. This wrapper is written without parameter checking. All parameters are passed via the arugment parameter that is passed in the constructor. See SYNOPSIS. For exonerate parameters, run exonerate --help for more details.
The tests have been shown to pass with exonorate versions 2.0 - 2.2.
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
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 track the bugs and their resolution. Bug reports can be submitted via the web:
http://redmine.open-bio.org/projects/bioperl/
Email shawnh-at-stanford.edu
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 : new Usage : my $factory= Bio::Tools::Run::Phrap->new(); Function: creates a new Phrap factory Returns: Bio::Tools::Run::Phrap 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 : my $feats = $factory->run($seq) Function: Runs Phrap Returns : An array of Bio::SeqFeature::Generic objects Args : A Bio::PrimarySeqI
Title : _input Usage : $factory->_input($seqFile) Function: get/set for input file Returns : Args :
Title : _run Usage : $factory->_run() Function: Makes a system call and runs Phrap Returns : An array of Bio::SeqFeature::Generic objects Args :
Title : _writeInput Usage : $factory->_writeInput($query,$target) Function: Creates a file from the given seq object Returns : A string(filename) Args : Bio::PrimarySeqI
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 :
| 2018-09-14 | perl v5.26.2 |