Bio::Tools::Run::Alignment::Exonerate(3pm) User Contributed Perl Documentation Bio::Tools::Run::Alignment::Exonerate(3pm)
NAME
Bio::Tools::Run::Alignment::Exonerate
SYNOPSIS
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 $hsp->start." ".$hsp->end."
";
}
}
}
DESCRIPTION
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.
PROGRAM VERSIONS
The tests have been shown to pass with exonorate versions 2.0 - 2.2.
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://redmine.open-bio.org/projects/bioperl/
AUTHOR - Shawn Hoon
Email shawnh-at-stanford.edu
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 :
new
Title : new
Usage : my $factory= Bio::Tools::Run::Phrap->new();
Function: creates a new Phrap factory
Returns: Bio::Tools::Run::Phrap
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 : my $feats = $factory->run($seq)
Function: Runs Phrap
Returns : An array of Bio::SeqFeature::Generic objects
Args : A Bio::PrimarySeqI
_input
Title : _input
Usage : $factory->_input($seqFile)
Function: get/set for input file
Returns :
Args :
_run
Title : _run
Usage : $factory->_run()
Function: Makes a system call and runs Phrap
Returns : An array of Bio::SeqFeature::Generic objects
Args :
_writeInput
Title : _writeInput
Usage : $factory->_writeInput($query,$target)
Function: Creates a file from the given seq object
Returns : A string(filename)
Args : Bio::PrimarySeqI
_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 :
perl v5.12.3 2011-06-18 Bio::Tools::Run::Alignment::Exonerate(3pm)