/ 
Bio-Prospect-1.04
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/ Bio::Prospect::LocalClient

NAME

Bio::Prospect::LocalClient -- execute Prospect locally
$Id: LocalClient.pm,v 1.32 2003/11/18 19:45:45 rkh Exp $

SYNOPSIS

my $in = new Bio::SeqIO( -format=> 'Fasta', '-file' => $ARGV[0] );
my $po = new Bio::Prospect::Options( seq=>1, svm=>1, global_local=>1,
  templates=>['1alu', '1bgc','1eera']);
my $pf = new Bio::Prospect::LocalClient( {options=>$po );

while ( my $s = $in->next_seq() ) {
  my @threads = $pf->thread( $s );
}

DESCRIPTION

Bio::Prospect::LocalClient is runs Prospect locally. It is intended to be used to facilitate high-throughput protein sequence threading and as the server-side component of Bio::Prospect::SoapClient, with which it is API compatible.

ROUTINES & METHODS

new()

Name:      new()
Purpose:   constructor
Arguments: hash reference with following key/value pairs
 options => Bio::Prospect::Options object (required)
Returns:   Bio::Prospect::LocalClient

thread()

Name:      thread()
Purpose:   return a list of Thread objects
Arguments: scalar sequence or Bio::PrimarySeqI-derived object
Returns:   list of Bio::Prospect::Thread objects

thread_summary()

Name:      thread_summary()
Purpose:   return a list of ThreadSummary objects
Arguments: Bio::Seq object
Returns:   list of rospect2::ThreadSummary objects

xml()

Name:      xml()
Purpose:   return xml string 
Arguments: Bio::Seq object
Returns:   string

INTERNAL METHODS & ROUTINES

The following functions are documented for developers' benefit. THESE SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE. YOU'VE BEEN WARNED.

_get_svm_scores()

Name:      _get_svm_scores()
Purpose:   return a hash of svm scores from a prospect sort file
Arguments: sort filename
Returns:   hash
::_thread_to_file( Bio::Seq | scalar )

Thread one sequence in the Bio::Seq object or the scalar string. The xml ouptut filename is returned. Threading results are cached by sequence for the lifetime of the LocalClient object. See also ::thread.

::_thread1( filename )

Threads the fasta-formatted sequence in filename which is passed directly to prospect. The name of a temporary file which contains the raw xml output is returned. This method will work with multiple sequences in filename, but other routines in this module will not understand multi-query xml output reliably. Most callers should use thread() instead.

_hasSvmScore()

Name:      _hasSvmScore()
Purpose:   check whether the prospect xml file already contains a svmScore tag
Arguments: prospect xml file
Returns:   1 (has svm score) or 0 (no svm score)

_output_svm_score()

Name:      _output_svm_score()
Purpose:   output the svm score in the propsect output file
Arguments: prospect xml file, prospect sort file
Returns:   prospect xml file with svm score

_sort1()

Name:      _sort1()
Purpose:   run sortProspect on threading file
Arguments: prospect xml file
Returns:   filename of sortProspect results
::_prepare_options()

Prepares temporary files based on options (e.g., writes a temporary `tfile') and generates an array of command line options in @{$self->{commandline}}. Args 1 and 2 are input and output respectively and MUST be sprintf'd before use. See thread_1_file().

SEE ALSO

Bio::Prospect::Options, Bio::Prospect::File, Bio::Prospect::Client, Bio::Prospect::SoapClient, Bio::Prospect::Thread, Bio::Prospect::ThreadSummary

http://www.bioinformaticssolutions.com/