Bio::Tools::Run::Analysis Bio::Tools::Run::Analysis is a Perl module representing any (remote or local) analysis tool.
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Perl module perl analyzer analysis tool bioperl Bioperl class

Bio::Tools::Run::Analysis Description

Bio::Tools::Run::Analysis is a Perl module representing any (remote or local) analysis tool. Bio::Tools::Run::Analysis is a Perl module representing any (remote or local) analysis tool.SYNOPSIS # run analysis 'seqret' using a default location and a default # access method (which means using a Web Service at EBI) use Bio::Tools::Run::Analysis; print new Bio::Tools::Run::Analysis (-name => 'edit::seqret') ->wait_for ({ sequence_direct_data => 'tatatacgtatacga', osformat => 'embl' }) ->result ('outseq'); # run a longer job without waiting for its completion use Bio::Tools::Run::Analysis; my $job = new Bio::Tools::Run::Analysis (-name => 'edit::seqret') ->run ({ sequence_direct_data => 'tatatacgtatacga', osformat => 'embl' }); # ...and after a while $job->result ('outseq'); # get all results in the same invocation (as a hash reference # with result names as keys) - let the module decide which # results are binary (images in this examples) and save those # in file (or files); it also shows how to tell that the module # should read input data from a local file first use Bio::Tools::Run::Analysis; my $results = new Bio::Tools::Run::Analysis (-name => 'alignment_multiple::prettyplot') ->wait_for ( { msf_direct_data => '@/home/testdata/my.seq' } ) ->results ('?'); use Data::Dumper; print Dumper ($results); # get names, types of all inputs and results, # get short and detailed (in XML) service description use Bio::Tools::Run::Analysis; my $service = new Bio::Tools::Run::Analysis (-name => 'edit::seqret'); my $hash1 = $service->input_spec; my $hash2 = $service->result_spec; my $hash3 = $service->analysis_spec; my $xml = $service->describe; # get current job status use Bio::Tools::Run::Analysis; print new Bio::Tools::Run::Analysis (-name => 'edit::seqret') ->run ( { #...input data... } ) ->status; # run a job and print its job ID, keep the job un-destroyed use Bio::Tools::Run::Analysis; my $job = new Bio::Tools::Run::Analysis (-name => 'edit::seqret', -destroy_on_exit => 0) ->run ( { sequence_direct_data => '@/home/testdata/mzef.seq' } ); print $job->id . "n"; # ...it prints (for example): # edit::seqret/c8ef56:ef535489ac:-7ff4 # ...in another time, on another planet, you may say use Bio::Tools::Run::Analysis; my $job = new Bio::Tools::Run::Analysis::Job (-name => 'edit::seqret', -id => 'edit::seqret/c8ef56:ef535489ac:-7ff4'); print join ("n", $job->status, 'Finished: ' . $job->ended (1), # (1) means 'formatted' 'Elapsed time: ' . $job->elapsed, $job->last_event, $job->result ('outseq') ); # ...or you may achieve the same keeping module # Bio::Tools::Run::Analysis::Job invisible use Bio::Tools::Run::Analysis; my $job = new Bio::Tools::Run::Analysis (-name => 'edit::seqret') ->create_job ('edit::seqret/c8ef56:ef535489ac:-7ff4'); print join ("n", $job->status, # ... ); # ...and later you may free this job resources $job->remove; # # --- See DESCRIPTION for using generator 'applmaker.pl': # Requirements: · Perl

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