Bio::Tools::Run::ERPINUser Contributed Perl DocumentaBio::Tools::Run::ERPIN(3)NAMEBio::Tools::Run::ERPIN - Wrapper for local execution of the ERPIN suite
of programs.
SYNOPSIS
#run
my @params = (
trset => 'BL.erpin',
region => [1, 10],
# Set up search strategy this way...
strategy => [ 'umask' => [1, 2],
'umask' => [1, 2, 3, 4],
'umask' => [1, 2, 3, 4, 5, 6],
'nomask',
'cutoff' => [0, 10, 15, 20]
]
# or use a simple string...
#strategy => '‐umask 4 ‐add 5 -nomask -cutoff 0 10 15',
pcw => 100
);
my $factory = Bio::Tools::Run::ERPIN->new(-program =>'erpin',
@params);
# Pass the factory a Bio::Seq object or a file name
# Returns a Bio::SearchIO object
#my $search = $factory->run("B_sub.fas");
my $search = $factory->run($seq);
my @feat;
while (my $result = $searchio->next_result){
while(my $hit = $result->next_hit){
while (my $hsp = $hit->next_hsp){
print join("\t", ( $r->query_name,
$hit->name,
$hsp->hit->start,
$hsp->hit->end,
$hsp->meta,
$hsp->score,
)), "\n";
}
}
}
DESCRIPTIONFEEDBACK
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://bugzilla.open-bio.org/
AUTHOR - Chris Fields
Email: cjfields-at-uiuc-dot-edu
CONTRIBUTORS
cjfields-at-uiuc-dot-edu
APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
new
Title : new
Usage : my $wrapper = Bio::Tools::Run::RNAMotif->new(@params)
Function: creates a new RNAMotif factory
Returns: Bio::Tools::Run::RNAMotif
Args : list of parameters
-tempfile => set tempfile flag (default 0)
-outfile_name => set file to send output to (default none)
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 :
version
Title : version
Usage : $v = $prog->version();
Function: Determine the version number of the program
Example :
Returns : float or undef
Args : none
run
Title : run
Usage : $obj->run($seqFile)
Function: Runs ERPIN programs and returns Bio::SearchIO
Returns :
Args : Must pass Bio::PrimarySeqI's or file names
tempfile
Title : tempfile
Usage : $obj->tempfile(1)
Function: Set tempfile flag. When set, writes output to a tempfile; this
is overridden by outfile_name() if set
Returns : Boolean setting (or undef if not set)
Args : [OPTIONAL] Boolean
_run
Title : _run
Usage : $obj->_run()
Function: Internal(not to be used directly)
Returns :
Args :
_setparams
Title : _setparams
Usage : Internal function, not to be called directly
Function: creates a string of params to be used in the command string
Example :
Returns : string of params
Args :
_writeSeqFile
Title : _writeSeqFile
Usage : obj->_writeSeqFile($seq)
Function: Internal(not to be used directly)
Returns : writes passed Seq objects to tempfile, to be used as input
for program
Args :
perl v5.14.1 2011-07-21 Bio::Tools::Run::ERPIN(3)
