Bio::Prospect::LocalClient -- execute Prospect locally $Id: LocalClient.pm,v 1.32 2003/11/18 19:45:45 rkh Exp $
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 ); }
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.
Name: new() Purpose: constructor Arguments: hash reference with following key/value pairs options => Bio::Prospect::Options object (required) Returns: Bio::Prospect::LocalClient
Name: thread() Purpose: return a list of Thread objects Arguments: scalar sequence or Bio::PrimarySeqI-derived object Returns: list of Bio::Prospect::Thread objects
Name: thread_summary() Purpose: return a list of ThreadSummary objects Arguments: Bio::Seq object Returns: list of rospect2::ThreadSummary objects
Name: xml() Purpose: return xml string Arguments: Bio::Seq object Returns: string
The following functions are documented for developers' benefit. THESE SHOULD NOT BE CALLED OUTSIDE OF THIS MODULE. YOU'VE BEEN WARNED.
Name: _get_svm_scores() Purpose: return a hash of svm scores from a prospect sort file Arguments: sort filename Returns: hash
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.
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.
filename
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)
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
Name: _sort1() Purpose: run sortProspect on threading file Arguments: prospect xml file Returns: filename of sortProspect results
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().
Bio::Prospect::Options, Bio::Prospect::File, Bio::Prospect::Client, Bio::Prospect::SoapClient, Bio::Prospect::Thread, Bio::Prospect::ThreadSummary
http://www.bioinformaticssolutions.com/
To install Bio::Prospect::File, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Prospect::File
CPAN shell
perl -MCPAN -e shell install Bio::Prospect::File
For more information on module installation, please visit the detailed CPAN module installation guide.