NAME¶
Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications
SYNOPSIS¶
use Bio::Factory::EMBOSS;
# get an EMBOSS application object from the EMBOSS factory
$factory = Bio::Factory::EMBOSS->new();
$application = $factory->program('embossversion');
# run the application with an optional hash containing parameters
$result = $application->run(); # returns a string or creates a file
print $result . "\n";
$water = $factory->program('water');
# here is an example of running the application
# water can compare 1 seq against 1->many sequences
# in a database using Smith-Waterman
my $seq_to_test; # this would have a seq here
my @seqs_to_check; # this would be a list of seqs to compare
my $wateroutfile = 'out.water';
$water->run({-sequencea => $seq_to_test,
-seqall => \@seqs_to_check,
-gapopen => '10.0',
-gapextend => '0.5',
-outfile => $wateroutfile});
# now you might want to get the alignment
use Bio::AlignIO;
my $alnin = Bio::AlignIO->new(-format => 'emboss',
-file => $wateroutfile);
while ( my $aln = $alnin->next_aln ) {
# process the alignment -- these will be Bio::SimpleAlign objects
}
DESCRIPTION¶
The EMBOSSApplication class can represent EMBOSS any program. It is created by a
Bio::Factory::EMBOSS object.
If you want to check command line options before sending them to the program set
$prog->verbose to positive integer. The ADC description of the available
command line options is then parsed in and compared to input.
See also Bio::Factory::EMBOSS and Bio::Tools::Run::EMBOSSacd.
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 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 - Heikki Lehvaslaiho¶
Email heikki-at-bioperl-dot-org
CONTRIBUTORS¶
Email: jason-AT-bioperl_DOT_org
APPENDIX¶
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
run¶
Title : run
Usage : $embossapplication->run($attribute_hash)
Function: Runs the EMBOSS program.
Returns : string or creates files for now; will return objects!
Args : hash of input to the program
acd¶
Title : acd
Usage : $embossprogram->acd
Function: finds out all the possible qualifiers for this
EMBOSS application. They can be used to debug the
options given.
Throws :
Returns : boolean
Args :
name¶
Title : name
Usage : $embossprogram->name
Function: sets/gets the name of the EMBOSS program
Setting is done by the EMBOSSFactory object,
you should only get it.
Throws :
Returns : name string
Args : None
descr¶
Title : descr
Usage : $embossprogram->descr
Function: sets/gets the descr of the EMBOSS program
Setting is done by the EMBOSSFactory object,
you should only get it.
Throws :
Returns : description string
Args : None
group¶
Title : group
Usage : $embossprogram->group
Function: sets/gets the group of the EMBOSS program
Setting is done by the EMBOSSFactory object,
you should only get it.
If the application is assigned into a subgroup
use l<subgroup> to get it.
Throws :
Returns : string, group name
Args : group string
subgroup¶
Title : subgroup
Usage : $embossprogram->subgroup
Function: sets/gets the subgroup of the EMBOSS program
Setting is done by the EMBOSSFactory object,
you should only get it.
Throws :
Returns : string, subgroup name; undef if not defined
Args : None
program_dir¶
Title : program_dir
Usage :
Function: Required by WrapperBase
Throws :
Returns : Name of directory with EMBOSS programs
Args :
program_path¶
Title : program_path
Usage :
Function: Required by WrapperBase
Throws :
Returns : Full path of program
Args :
executable¶
Title : executable
Usage :
Function: Required by WrapperBase
Throws :
Returns : Name of program
Args :