SYNOPSIS

# parameters which are switches are set with any value that evals TRUE,
# others are set to a specific value
my $factory = Bio::Tools::Run::Infernal->new(@params);
# run cmalign|cmbuild|cmsearch|cmscore|cmemit directly as a wrapper method
# this resets the program flag if previously set
$factory->cmsearch(@seqs); # searches Bio::PrimarySeqI's based on set cov. model
# saves output to optional outfile_name, returns
# Bio::SearchIO
# only values which are allowed for a program are set, so one can use the same
# wrapper for the following...
$factory->cmalign(@seqs); # aligns Bio::PrimarySeqI's to a set cov. model,
# --merge option allows two alignments generated
# from the same CM to be merged.
# output to outfile_name, returns Bio::AlignIO
$factory->cmscore(); # scores set cov. model against Bio::PrimarySeqI,
# output to outfile_name/STDOUT.
$factory->cmbuild($aln); # builds covariance model based on alignment
# CM to outfile_name or model_file (one is required
# here), output to STDOUT.
$factory->cmemit(); # emits sequence from specified cov. model;
# set one if no file specified. output to
# outfile_name, returns Bio::SeqIO or (if -a is set)
# Bio::AlignIO
$factory->cmcalibrate($file); # calibrates specified cov. model; output to
# STDOUT
$factory->cmstat($file); # summary stats for cov. model; set one if no file
# specified; output to STDOUT
# run based on the setting of the program parameter
my $factory = Bio::Tools::Run::Infernal->new(-program => 'cmsearch',
@params);
my $search = $factory->run($seq);
# using cmsearch returns a Bio::SearchIO object
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";
}
}
}

DESCRIPTION

Wrapper module for Sean Eddy's Infernal suite of programs. The current implementation runs cmsearch, cmcalibrate, cmalign, cmemit, cmbuild, cmscore, and cmstat. cmsearch will return a Bio::SearchIO, cmemit a Bio::SeqIO/AlignIO, and cmalign a Bio::AlignIO. All others send output to STDOUT. Optionally, any program's output can be redirected to outfile_name.

We HIGHLY suggest upgrading to Infernal 1.0. In that spirit, this wrapper now supports parameters for Infernal 1.0 only; for wrapping older versions of Infernal we suggest using the version of Bio::Tools::Run::Infernal that came with previous versions of BioPerl-run.

NOTE: Due to conflicts in the way Infernal parameters are now formatted vs. subroutine naming in Perl (specifically the inclusion of hyphens) and due to the very large number of parameters available, setting and resetting parameters via set_parameters() and reset_parameters() is required. All valid parameters can be set, but only ones valid for the executable set via program()/program_name() are used for calling the executables, the others are silently ignored.

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.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

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 - 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::Infernal->new(@params)
 Function: creates a new Infernal factory
 Returns:  Bio::Tools::Run::Infernal wrapper
 Args    : list of parameters

program

 Title   :  program
 Usage   :  $obj->program()
 Function:  Set the program called when run() is used.  Synonym of
            program_name()
 Returns :  String (program name)
 Args    :  String (program name)
 Status  :  Unstable (may delegate to program_name, which is the interface method)

program_name

 Title   : program_name
 Usage   : $factory>program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

model_file

 Title   :  model_file
 Usage   :  $obj->model_file()
 Function:  Set the model file used when run() is called.
 Returns :  String (file location of covariance model)
 Args    :  String (file location of covariance model)

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 (uses cmsearch)
 Example :
 Returns : float or undef
 Args    : none

run

 Title   :   run
 Usage   :   $obj->run($seqFile)
 Function:   Runs Infernal and returns Bio::SearchIO
 Returns :   A Bio::SearchIO
 Args    :   A Bio::PrimarySeqI or file name

Specific program interface methods

cmsearch

 Title   :   cmsearch
 Usage   :   $obj->cmsearch($seqFile)
 Function:   Runs Infernal cmsearch and returns Bio::SearchIO
 Returns :   A Bio::SearchIO
 Args    :   Bio::PrimarySeqI or file name

cmalign

 Title   :   cmalign
 Usage   :   $obj->cmalign($seqFile)
 Function:   Runs Infernal cmalign and returns Bio::AlignIO
 Returns :   A Bio::AlignIO
 Args    :   Bio::PrimarySeqI or file name

cmemit

 Title   :   cmemit
 Usage   :   $obj->cmemit($modelfile)
 Function:   Runs Infernal cmemit and returns Bio::AlignIO
 Returns :   A Bio::AlignIO
 Args    :   None; set model_file() to use a specific model

cmbuild

 Title   :   cmbuild
 Usage   :   $obj->cmbuild($alignment)
 Function:   Runs Infernal cmbuild and saves covariance model
 Returns :   1 on success (no object for covariance models)
 Args    :   Bio::AlignIO with structural information (such as from Stockholm
             format source) or alignment file name

cmscore

 Title   :   cmscore
 Usage   :   $obj->cmscore($seq)
 Function:   Runs Infernal cmscore and saves output
 Returns :   None
 Args    :   None; set model_file() to use a specific model

cmcalibrate

 Title   :   cmcalibrate
 Usage   :   $obj->cmcalibrate('file')
 Function:   Runs Infernal calibrate on specified CM
 Returns :   None
 Args    :   None; set model_file() to use a specific model

cmstat

 Title   :   cmstat
 Usage   :   $obj->cmstat($seq)
 Function:   Runs Infernal cmstat and saves output
 Returns :   None
 Args    :   None; set model_file() to use a specific model

Bio::ParameterBaseI-specific methods

These methods are part of the Bio::ParameterBaseI interface

set_parameters

 Title   : set_parameters
 Usage   : $pobj->set_parameters(%params);
 Function: sets the parameters listed in the hash or array
 Returns : None
 Args    : [optional] hash or array of parameter/values.  These can optionally
           be hash or array references
 Note    : This only sets parameters; to set methods use the method name

reset_parameters

 Title   : reset_parameters
 Usage   : resets values
 Function: resets parameters to either undef or value in passed hash
 Returns : none
 Args    : [optional] hash of parameter-value pairs

validate_parameters

 Title   : validate_parameters
 Usage   : $pobj->validate_parameters(1);
 Function: sets a flag indicating whether to validate parameters via
           set_parameters() or reset_parameters()
 Returns : Bool
 Args    : [optional] value evaluating to True/False
 Note    : Optionally implemented method; up to the implementation on whether
           to automatically validate parameters or optionally do so

parameters_changed

 Title   : parameters_changed
 Usage   : if ($pobj->parameters_changed) {...}
 Function: Returns boolean true (1) if parameters have changed
 Returns : Boolean (0 or 1)
 Args    : None
 Note    : This module does not run state checks, so this always returns True

available_parameters

 Title   : available_parameters
 Usage   : @params = $pobj->available_parameters()
 Function: Returns a list of the available parameters
 Returns : Array of parameters
 Args    : [optional] name of executable being used; defaults to returning all
           available parameters

get_parameters

 Title   : get_parameters
 Usage   : %params = $pobj->get_parameters;
 Function: Returns list of set key-value pairs, parameter => value
 Returns : List of key-value pairs
 Args    : [optional]
           'full' - this option returns everything associated with the parameter
                    as an array ref value; that is, not just the value but also
                    the value, type, and prefix. Default is value only.
           'valid'- same a 'full', but only returns the grouping valid for the
                    currently set executable

to_* methods

All to_* methods are implementation-specific

to_exe_string

 Title   : to_exe_string
 Usage   : $string = $pobj->to_exe_string;
 Function: Returns string (command line string in this case)
 Returns : String 
 Args    :

_writeSeqFile

 Title   :   _writeSeqFile
 Usage   :   obj->_writeSeqFile($seq)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :

_writeAlignFile

 Title   :   _writeAlignFile
 Usage   :   obj->_writeAlignFile($seq)
 Function:   Internal(not to be used directly)
 Returns :
 Args    :