Provided by: bioperl-run_1.7.3-8_all bug


       panalysis.PLS - An example/tutorial script how to access analysis tools


        # run an analysis with your sequence in a local file
          ./panalysis.PLS -n 'edit.seqret'-w -r \

        See more examples in the text below.


       A client showing how to use "Bio::Tools::Run::Analysis" module, a module for executing and
       controlling local or remote analysis tools.  It also calls methods from the
       "Bio::Tools::Run::AnalysisFactory" module, a module providing lists of available analyses.

       Primarily, this client is meant as an example how to use analysis modules, and also to
       test them. However, because it has a lot of options in order to cover as many methods as
       possible, it can be also used as a fully functional command-line client for accessing
       various analysis tools.

   Defining location and access method
       "panalysis.PLS" is independent on the access method to the remote analyses (the analyses
       running on a different machines). The method used to communicate with the analyses is
       defined by the "-A" option, with the default value soap. The other possible values (not
       yet supported, but coming soon) are corba and local.

       Each access method may have different meaning for parameter "-l" defining a location of
       services giving access to the analysis tools. For example, the soap access expects a URL
       of a Web Service in the "-l" option, while the corba access may find here a stringified
       Interoperable Object Reference (IOR).

       A default location for the soap access is "" which
       represents services running at European Bioinformatics Institute on top of over hundred
       EMBOSS analyses (and on top of few others).

   Available analyses
       "panalysis.PLS" can show a list of available analyses (from the given location using given
       access method). The "-L" option shows all analyses, the "-c" option lists all available
       categories (a category is a group of analyses with similar functionality or processing
       similar type of data), and finally the "-C" option shows only analyses available within
       the given category.

       Note, that all these functions are provided by module "Bio::Tools::Run::AnalysisFactory"
       (respectively, by one of its access-dependent sub-classes). The module has also a factory
       method "create_analysis" which is not used by this script.

       A "service" is a higher level of abstraction of an analysis tool. It understands a well
       defined interface (module "Bio::AnalysisI", a fact which allows this script to be
       independent on the access protocol to various services.

       The service name must be given by the "-n" option. This option can be omitted only if you
       invoked just the "factory" methods (described above).

       Each service (representing an analysis tool, a program, or an application) has its
       description, available by using options "-a" (analysis name, type, etc.), "-i", "-I"
       (specification of analysis input data, most important are their names), and "-o", "-O"
       (result names and their types). The option "-d" gives the most detailed description in the
       XML format.

       The service description is nice but the most important is to use the service for invoking
       an underlying analysis tool. For each invocation, the service creates a "job" and feeds it
       with input data. There are three stages: (a) create a job, (b) run the job, and (c) wait
       for its completion. Correspondingly. there are three options: the "-b" which just creates
       (builds) a job, the "-x" which creates a job and executes it, and finally "-w" which
       creates a job, runs it and blocks the client until the job is finished. Always only one of
       these options is used (so it does not make sense to use more of them, the "panalysis.PLS"
       priorities them in the order "-x", "-w", and "-b").

       All of these options take input data from the command-line (see next section about it) and
       all of them return (internally) an object representing a job. There are many methods
       (options) dealing with the job objects (see one after next section about them).

       Last note in this section: the "-b" option is actually optional - a job is created even
       without this option when there are some input data found on the command-line. You have to
       use it, however, if you do not pass any data to an analysis tool (an example would be the
       famous "Classic::HelloWorld" service).

   Input data
       Input data are given as name/value pairs, put on the command-line with equal sign between
       name and value. If the value part starts with an un-escaped character "@", it is used as a
       local file name and the "panalysis.PLS" reads the file and uses its contents instead.

          panalysis.PLS -n edit.seqret -w -r
                        sequence_direct_data='tatatctcccc' osformat=embl

          panalysis.PLS ...

       The names of input data come from the "input specification" that can be shown by the "-i"
       or "-I" options. The input specification (when using option "-I") shows also - for some
       inputs - a list of allowed values.  The specification, however, does not tell what input
       data are mutually exclusive, or what other constrains apply. If there is a conflict, an
       error message is produced later (before the job starts).

       Input data are used when any of the options "-b", "-x", or "-w" is present, but option
       "-j" is not present (see next section about this job option).

       Each service (defined by a name given in the "-n" option) can be executed one or more
       times, with the same, but usually with different input data. Each execution creates a job
       object. Actually, the job is created even before execution (remember that option "-b"
       builds a job but does not execute it yet).

       Any job, executed or not, is persistent and can be used again later from another
       invocation of the "panalysis.PLS" script. Unless you explicitly destroy the job using
       option "-z".

       A job created by options "-b", "-x" and "-w" (and by input data) can be accessed in the
       same "panalysis.PLS" invocation using various job-related options, the most important are
       "-r" and "-R" for retrieving results from the finished job.

       However, you can also re-create a job created by a previous invocation. Assuming that you
       know the job ID (the "panalysis.PLS" prints it always on the standard error when a new job
       is created), use option "-j" to re-create the job.


          ./panalysis.PLS -n 'edit.seqret'

       It prints:

          JOB ID: edit.seqret/bb494b:ef55e47c99:-8000

       Next invocation (asking to run the job, to wait for its completion and to show job status)
       can be:

          ./panalysis.PLS -n 'edit.seqret'
                        -j edit.seqret/bb494b:ef55e47c99:-800
                        -w -s

       And again later another invocation can ask for results:

          ./panalysis.PLS -n 'edit.seqret'
                        -j edit.seqret/bb494b:ef55e47c99:-800

       Here is a list of all job options (except for results, they are in the next section):

       Job execution and termination
           There are the same options "-x" and "-w" for executing a job and for executing it and
           waiting for its completion, as they were described above. But now, the options act on
           a job given by the "-j" option, now they do not use any input data from the command-
           line (the input data had to be used when the job was created).

           Additionally, there is a "-k" option to kill a running job.

       Job characteristics
           Other options tell about the job status ("-s", about the job execution times ("-t" and
           "-T", and about the last available event what happened with the job ("-e"). Note that
           the event notification is not yet fully implemented, so this option will change in the
           future to reflect more notification capabilities.

       Of course, the most important on the analysis tools are their results. The results are
       named (in the similar way as the input data) and they can be retrieved all in one go using
       option "-r" (so you do not need to know their names actually), or by specifying (all or
       some) result names using the "-R" option.

       If a result does not exist (either not yet, or the name is wrong) an undef value is
       returned (no error message produced).

       Some results are better to save directly into files instead to show them in the terminal
       window (this applies to the binary results, mostly containing images). The "panalysis.PLS"
       helps to deal with binary results by saving them automatically to local files (actually it
       is the module "Bio::Tools::Run::Analysis" and its submodules who do help with the binary

       So why not to use a traditional shell re-direction to a file? There are two reasons.
       First, a job can produce more than one result, so they would be mixed together. But
       mainly, because each result can consist of several parts whose number is not known in
       advance and which cannot be mixed together in one file. Again, this is typical for the
       binary data returning images - an invocation can produce many images.

       The "-r" option retrieves all available results and treat them as described by the '?'
       format below.

       The "-R" option has a comma-separated list of result names, each of the names can be
       either a simple name (as specified by the "result specification" obtainable using the "-o"
       or "-O" options), or a equal-sign-separated name/format construct suggesting what to do
       with the result. The possibilities are:

           It prints given result on the standard output.

           It saves the given result into given file.

           It saves the given result into a file whose name is automatically invented, and it
           guarantees that the same name will not be used in the next invocation.

           It saves the given result into a file whose name is given by the "template". The
           template can contain several strings which are substituted before using it as the

           Any '*'
               Will be replaced by a unique number

           $ANALYSIS or ${ANALYSIS}
               Will be replaced by the current analysis name

           $RESULT or ${RESULT}
               Will be replaced by the current result name

               How to tell what to do with results? Each result name

           Additionally, a template can be given as an environment variable
           "RESULT_FILENAME_TEMPLATE". Such variable is used for any result having in its format
           a simple "?" or "@" character.

           It first decides whether the given result is binary or not. Then, the binary results
           are saved into local files whose names are automatically invented, the other results
           are sent to the standard output.

           The same as above but the filenames for binary files are deduced from the given
           template (using the same rules as described above).


          -R report
          -R report,outseq
          -R Graphics_in_PNG=@
          -R Graphics_in_PNG=@$ANALYSIS-*-$RESULT

       Note that the result formatting will be enriched in the future by using existing data type
       parsers in bioperl.


   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send
       your comments and suggestions preferably to the Bioperl mailing list.  Your participation
       is much appreciated.
                  - General discussion  - About the mailing lists

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their
       resolution. Bug reports can be submitted via the web:


       Martin Senger (


       Copyright (c) 2003, Martin Senger and EMBL-EBI.  All Rights Reserved.

       This script is free software; you can redistribute it and/or modify it under the same
       terms as Perl itself.


       This software is provided "as is" without warranty of any kind.


       None known at the time of writing this.