| Bio::Tools::Run::EMBOSSApplication(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::EMBOSSApplication(3pm) |
Bio::Tools::Run::EMBOSSApplication - class for EMBOSS Applications
# Get an EMBOSS factory
use Bio::Factory::EMBOSS;
$f = Bio::Factory::EMBOSS -> new();
# Get an EMBOSS application object from the factory
$water = $f->program('water') || die "Program not found!\n";
# Here is an example of running the application - water can
# compare 1 sequence against 1 or more sequences using Smith-Waterman.
# Pass a Sequence object and a reference to an array of objects.
my $wateroutfile = 'out.water';
$water->run({-asequence => $seq_object,
-bsequence => \@seq_objects,
-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
}
The EMBOSSApplication class can represent any EMBOSS 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.
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
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 heikki-at-bioperl-dot-org
Email: jason-AT-bioperl_DOT_org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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 :
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
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
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
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
Title : program_dir Usage : Function: Required by WrapperBase Throws : Returns : Name of directory with EMBOSS programs Args :
Title : program_path Usage : Function: Required by WrapperBase Throws : Returns : Full path of program Args :
Title : executable Usage : Function: Required by WrapperBase Throws : Returns : Name of program Args :
| 2021-01-06 | perl v5.32.0 |