09-03-2010
hmm, what I would like ideally is this (say I'm replacing JO with BO)
my file to run sed on looks like this (as an example):
akdjfdkl sdjfklsjdf jsdfkljsf JO KSJDFKDFJLJOdsjfskldjf dsjfkljsfl <---- first JO on this line should be replaced by sed, second one should not because it forms part of a word
akdjalsd@JO <--- JO should be replaced here by sed
sdfkjdslfjsl@dfdsf_JO <----- and here
JO <---- and here
jo <----- and here
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LEARN ABOUT DEBIAN
bio::tools::run::genemark
Bio::Tools::Run::Genemark(3pm) User Contributed Perl Documentation Bio::Tools::Run::Genemark(3pm)
NAME
Bio::Tools::Run::Genemark - Wrapper for local execution of the GeneMark family of programs.
SYNOPSIS
# GeneMark.hmm (prokaryotic)
my $factory =
Bio::Tools::Run::Genemark->new('-program' => 'gmhmmp',
'-m' => 'model.icm');
# Pass the factory Bio::Seq objects
# returns a Bio::Tools::Genemark object
my $genemark = $factory->run($seq);
DESCRIPTION
Wrapper module for the GeneMark family of programs. Should work with all flavors of GeneMark.hmm at least, although only the prokaryotic
version has been tested.
General information about GeneMark is available at <http://exon.gatech.edu/GeneMark/>.
Contact information for licensing inquiries is available at: <http://opal.biology.gatech.edu/GeneMark/contact.html>
Note that GeneMark.hmm (prokaryotic at least) will only process the first sequence in a fasta file (if you run() more than one sequence at
a time, only the first will be processed).
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 - Mark Johnson
Email: mjohnson-at-watson-dot-wustl-dot-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: gets/sets the program name
Returns: string
Args : string
program_dir
Title : program_dir
Usage : $factory->program_dir()
Function: gets/sets the program dir
Returns: string
Args : string
new
Title : new
Usage : $genemark->new(@params)
Function: creates a new Genemark factory
Returns: Bio::Tools::Run::Genemark
Args :
run
Title : run
Usage : $obj->run($seq_file)
Function: Runs Genemark
Returns : A Bio::Tools::Genemark object
Args : An array of Bio::PrimarySeqI objects
_run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns : An instance of Bio::Tools::Genemark
Args : file name, sequence identifier (optional)
_write_seq_file
Title : _write_seq_file
Usage : obj->_write_seq_file($seq) or obj->_write_seq_file(@seq)
Function: Internal(not to be used directly)
Returns : Name of a temp file containing program output
Args : One or more Bio::PrimarySeqI objects
perl v5.12.3 2011-06-18 Bio::Tools::Run::Genemark(3pm)