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# `intermediate_example` – A real-world example

See here for an overview and explanations for this code.

The code for this example is in the test subdirectory of the `ruffus` module:

> `ruffus/test/intermediate_example.py`

The data is at:

> `ruffus/test/data_for_intermediate_example`

## Programme options:

> `--help````,` `-h```
>   show help message

### To specify tasks:

> `--target_tasks` `TARGET_TASK``,` `-t` `TARGET_TASK`

>   Target task(s) of pipeline. TARGET_TASK can be

>   - `gwas_simulation`
>   - `statistical_summary`

>   For example:

>       intermediate_example.py -t statistical_summary

> `--forced_tasks` `FORCED_TASK``,` `-f` `FORCED_TASK`

>   Pipeline task(s) which will be run even if they are up to date.

>   For example:

>       intermediate_example.py -t gwas_simulation

> `--jobs` `N``,` `-j` `N`

>   > N specifies number of concurrent process running jobs in parallel

### To specify paths:

> `--gene_data_dir` `PATH``,` `-d` `PATH`
>   Directory with input data.
> `--simulation_data_dir` `PATH``,` `-s` `PATH`
>   Directory with input data.
> `--working_dir` `PATH``,` `-d` `PATH`
>   Direction in which ruffus will run.

### To print flowchart:

> `--dependency` `FILE``,` `-d` `file`
>   Print a dependency graph of the pipeline that would be executed to FILE, but do not execute it.
> `--dependency_graph_format` `FORMAT``,` `-F` `FORMAT`

>   Format of dependency graph file.

>   Can be:

>       * 'ps'
>           (PostScript)

>       * 'svg'

>       * 'svgz'
>           (Structured Vector Graphics),

>       * 'png'

>       * 'gif'
>            (bitmap  graphics)

> `--just_print````,` `-n```
>   Print a description of the jobs that would be executed, but do not execute them.

## Code:

    #!/usr/bin/env python
    """

        intermediate_example.py

            This script takes N pairs of input file pairs
                                    (with the suffices .gene and .gwas)
                              and runs them against M sets of simulation data
                                    (with the suffix .simulation)
            A summary per input file pair is then produced

        In pseudo-code:

            STEP_1:

            for n_file in NNN_pairs_of_input_files:
                for m_file in MMM_simulation_data:

                    [n_file.gene,
                     n_file.gwas,
                     m_file.simulation] -> n_file.m_file.simulation_res

            STEP_2:

            for n_file in NNN_pairs_of_input_files:

                n_file.*.simulation_res -> n_file.mean

    """

    import os, sys
    exe_path = os.path.split(os.path.abspath(sys.argv[0]))[0]
    from ruffus import *
    from time import sleep
    import random
    from itertools import izip

    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

    #   options

    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

    from optparse import OptionParser
    parser = OptionParser(version="%prog 1.0")
    parser.add_option("-t", "--target_tasks", dest="target_tasks",
                      action="append",
                      default = ["statistical_summary"],
                      metavar="JOBNAME",
                      type="string",
                      help="Target task(s) of pipeline.")
    parser.add_option("-f", "--forced_tasks", dest="forced_tasks",
                      action="append",
                      default = list(),
                      metavar="JOBNAME",
                      type="string",
                      help="Pipeline task(s) which will be included even if they are up to date.")
    parser.add_option("-j", "--jobs", dest="jobs",
                      default=5,
                      metavar="jobs",
                      type="int",
                      help="Specifies the number of jobs (commands) to run simultaneously.")

    parser.add_option("-g", "--gene_data_dir", dest="gene_data_dir",
                      default="%s/data_for_intermediate_example/genes" % exe_path,
                      metavar="PATH",
                      type="string",
                      help="Directory with gene data [*.genes / *.gwas].")
    parser.add_option("-s", "--simulation_data_dir", dest="simulation_data_dir",
                      default="%s/data_for_intermediate_example/simulation" % exe_path,
                      metavar="PATH",
                      type="string",
                      help="Directory with simulation data [*.simulation].")
    parser.add_option("-w", "--working_dir", dest="working_dir",
                      default="/working_dir",
                      metavar="PATH",
                      type="string",
                      help="Working directory.")

    parser.add_option("-v", "--verbose", dest = "verbose",
                      action="store_true", default=False,
                      help="Do not echo to shell but only print to log.")
    parser.add_option("-D", "--dependency", dest="dependency_file",
                      metavar="FILE",
                      type="string",
                      help="Print a dependency graph of the pipeline that would be executed "
                            "to FILE, but do not execute it.")
    parser.add_option("-F", "--dependency_graph_format", dest="dependency_graph_format",
                      metavar="FORMAT",
                      type="string",
                      default = 'svg',
                      help="format of dependency graph file. Can be 'ps' (PostScript), "+
                      "'svg' 'svgz' (Structured Vector Graphics), " +
                      "'png' 'gif' (bitmap  graphics) etc ")
    parser.add_option("-n", "--just_print", dest="just_print",
                        action="store_true", default=False,
                        help="Print a description of the jobs that would be executed, "
                            "but do not execute them.")

    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

    #   imports

    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

    import StringIO
    import re
    import operator
    import sys
    from collections import defaultdict
    import glob
    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

    #   Functions

    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

    #_________________________________________________________________________________________
    #
    #   get gene gwas file pairs
    #
    #_________________________________________________________________________________________
    def get_gene_gwas_file_pairs(  ):
        """
        Helper function to get all *.gene, *.gwas from the direction specified
            in --gene_data_dir

        Returns
            file pairs with both .gene and .gwas extensions,
            corresponding roots (no extension) of each file
        """

        gene_files = glob.glob(os.path.join(options.gene_data_dir, "*.gene"))
        gwas_files = glob.glob(os.path.join(options.gene_data_dir, "*.gwas"))

        common_roots = set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gene_files))
        common_roots &=set(map(lambda x: os.path.splitext(os.path.split(x)[1])[0], gwas_files))
        common_roots = list(common_roots)

        p = os.path; g_dir = options.gene_data_dir

        file_pairs = [[p.join(g_dir, x + ".gene"), p.join(g_dir, x + ".gwas")] for x in common_roots]

        return file_pairs, common_roots

    #_________________________________________________________________________________________
    #
    #   get simulation files
    #
    #_________________________________________________________________________________________
    def get_simulation_files(  ):
        """
        Helper function to get all *.simulation from the direction specified
            in --simulation_data_dir
            Returns
                file with .simulation extensions,
                corresponding roots (no extension) of each file
        """
        simulation_files = glob.glob(os.path.join(options.simulation_data_dir, "*.simulation"))
        simulation_roots =map(lambda x: os.path.splitext(os.path.split(x)[1])[0], simulation_files)
        return simulation_files, simulation_roots

    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

    #   Main logic

    #88888888888888888888888888888888888888888888888888888888888888888888888888888888888888888

    # get help string
    f =StringIO.StringIO()
    parser.print_help(f)
    helpstr = f.getvalue()
    (options, remaining_args) = parser.parse_args()

    working_dir = options.working_dir

    #_________________________________________________________________________________________
    #
    #   Step 1:
    #
    #        for n_file in NNN_pairs_of_input_files:
    #            for m_file in MMM_simulation_data:
    #
    #                [n_file.gene,
    #                 n_file.gwas,
    #                 m_file.simulation] -> working_dir/n_file.m_file.simulation_res
    #
    #_________________________________________________________________________________________
    def generate_simulation_params ():
        """
        Custom function to generate
        file names for gene/gwas simulation study
        """

        simulation_files, simulation_file_roots    = get_simulation_files()
        gene_gwas_file_pairs, gene_gwas_file_roots =  get_gene_gwas_file_pairs()

        for sim_file, sim_file_root in izip(simulation_files, simulation_file_roots):
            for (gene, gwas), gene_file_root in izip(gene_gwas_file_pairs, gene_gwas_file_roots):

                result_file = "%s.%s.simulation_res" % (gene_file_root, sim_file_root)
                result_file_path = os.path.join(working_dir, "simulation_results", result_file)

                yield [gene, gwas, sim_file], result_file_path, gene_file_root, sim_file_root, result_file

    #
    # mkdir: makes sure output directories exist before task
    #
    @follows(mkdir(options.working_dir, os.path.join(working_dir, "simulation_results")))
    @files(generate_simulation_params)
    def gwas_simulation(input_files, result_file_path, gene_file_root, sim_file_root, result_file):
        """
        Dummy calculation of gene gwas vs simulation data
        Normally runs in parallel on a computational cluster
        """
        (gene_file,
        gwas_file,
        simulation_data_file) = input_files

        simulation_res_file = open(result_file_path, "w")
        simulation_res_file.write("%s + %s -> %s\n" % (gene_file_root, sim_file_root, result_file))

    #_________________________________________________________________________________________
    #
    #   Step 2:
    #
    #       Statistical summary per gene/gwas file pair
    #
    #        for n_file in NNN_pairs_of_input_files:
    #            working_dir/simulation_results/n.*.simulation_res
    #               -> working_dir/n.mean
    #
    #_________________________________________________________________________________________
    def generate_statistical_summary_params():
        """
        Custom function to summarising simulation results files per gene / gwas file pair
        """
        gene_gwas_file_pairs, gene_gwas_file_roots =  get_gene_gwas_file_pairs()

        for (gene, gwas), gene_file_root in izip(gene_gwas_file_pairs, gene_gwas_file_roots):
                result_glob_spec = "%s.*.simulation_res" % (gene_file_root)
                result_files     = glob.glob(os.path.join(working_dir, "simulation_results", result_glob_spec))
                summary_file     = os.path.join(working_dir, gene_file_root + ".mean")

                yield result_files, summary_file

    @follows(gwas_simulation)
    @files(generate_statistical_summary_params)
    @posttask(lambda : sys.stdout.write("\nAll finished: hooray!!!\n"))
    def statistical_summary (result_files, summary_file):
        """
        Simulate statistical summary
        """

        summary_file = open(summary_file, "w")
        for f in result_files:
            summary_file.write(open(f).read())
        sleep(1)

    #888888888888888888888888888888888888888888888888888888888888888888888888888888888888888888
    #
    #   print pipeline or run pipeline
    #

    if options.just_print:
        pipeline_printout(sys.stdout, options.target_tasks, options.forced_tasks, long_winded=True)

    elif options.dependency_file:
        graph_printout (     open(options.dependency_file, "w"),
                             options.dependency_graph_format,
                             options.target_tasks,
                             options.forced_tasks)
    else:
        pipeline_run(options.target_tasks, options.forced_tasks, multiprocess = options.jobs)

### Navigation

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- modules |
- next |
- previous |
Ruffus v. 1.1.3b
- Home |
- Contents |
- Cheat sheet |
- Full tutorial |
- FAQ |
- Future plans |
- Search »