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 $hsp->start."\t".$hsp->end."\n";
}
}
}
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
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 :
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 :