Python prepend_paths Examples

Example #1

File: SConstruct_mcl.py Project: thebevrishot/proxigenomics

def make_cluster_input(outdir, c):

    source = [str(c['make_graph']['edges']), str(c['make_graph']['nodes'])]
    target = appconfig.prepend_paths(outdir, config['cluster']['input'])

    action = exec_env.resolve_action({
        'pbs': 'bin/pbsrun_MKMCL.sh {0[ctg_minlen]} $SOURCES.abspath $TARGET.abspath'.format(config),
        'sge': 'bin/sgerun_MKMCL.sh {0[ctg_minlen]} $SOURCES.abspath $TARGET.abspath'.format(config),
        'local': 'bin/makeMCLinput.py {0[ctg_minlen]} $SOURCES.abspath $TARGET.abspath'.format(config)
    })

    return 'output', env.Command(target, source, action)

Example #2

File: SConstruct_mcl.py Project: thebevrishot/proxigenomics

def do_cluster(outdir, c):
    # TODO run over both weighted/unweighted?
    source = c['make_cluster_input']['output']
    target = appconfig.prepend_paths(outdir, config['cluster']['output'])

    action = exec_env.resolve_action({
        'pbs': 'bin/pbsrun_MCL.sh {0[mcl_inflation]} $SOURCE.abspath $TARGET.abspath'.format(c),
        'sge': 'bin/sgerun_MCL.sh {0[mcl_inflation]} $SOURCE.abspath $TARGET.abspath'.format(c),
        'local': 'bin/mcl $SOURCE.abspath --abc -I {0[mcl_inflation]} -o $TARGET.abspath'.format(c)
    })

    return 'output', env.Command(target, source, action)

Example #3

File: SConstruct_srmcl.py Project: koadman/proxigenomics

def do_cluster(outdir, c):
    # TODO run over both weighted/unweighted?
    sources = [c['make_cluster_input']['nodemap'], c['do_cluster']['output']]
    target = appconfig.prepend_paths(outdir, config['cluster']['output'])

    action = exec_env.resolve_action({
        'pbs': 'bin/metisClToMCL.py $SOURCES.abspath $TARGET.abspath'.format(c),
        'sge': 'bin/metisClToMCL.py $SOURCES.abspath $TARGET.abspath'.format(c),
        'local': 'bin/metisClToMCL.py $SOURCES.abspath $TARGET.abspath'.format(c)
    })

    return 'output', env.Command(target, sources, action)

Example #4

def do_cluster(outdir, c):
    # TODO run over both weighted/unweighted?
    source = c['make_cluster_input']['output']
    target = appconfig.prepend_paths(outdir, config['cluster']['output'])

    action = exec_env.resolve_action({
        'pbs': 'bin/pbsrun_OCLUSTR.sh -i $SOURCE.abspath $TARGET.abspath',
        'sge': 'bin/sgerun_OCLUSTR.sh -i $SOURCE.abspath $TARGET.abspath',
        'local': 'bin/oclustr.py $SOURCE.abspath $TARGET.abspath'
    })

    return 'output', env.Command(target, source, action)

Example #5

File: SConstruct_srmcl.py Project: koadman/proxigenomics

def make_cluster_input(outdir, c):

    sources = [str(c['make_graph']['edges']), str(c['make_graph']['nodes'])]
    base_out = appconfig.prepend_paths(outdir, config['cluster']['input'])[0]
    targets = [base_out, base_out + '.nodemap']

    action = exec_env.resolve_action({
        'pbs': 'bin/pbsrun_MKMETIS.sh {0[ctg_minlen]} $SOURCES.abspath $TARGETS.abspath'.format(config),
        'sge': 'bin/sgerun_MKMETIS.sh {0[ctg_minlen]} $SOURCES.abspath $TARGETS.abspath'.format(config),
        'local': 'bin/edgeToMetis.py --fmt metis -m {0[ctg_minlen]} $SOURCES.abspath $TARGETS.abspath'.format(config)
    })

    return 'output', 'nodemap', env.Command(targets, sources, action)

Example #6

File: SConstruct_mcl.py Project: thebevrishot/proxigenomics

def make_graph(outdir, c):
    # add the root back in because we need to refer to the file
    ref_path = os.path.join(config['map_folder'], c['hic_path'])
    hic_bam = str(os.path.join(ref_path, config['hic2ctg']))

    source = hic_bam
    targets = appconfig.prepend_paths(outdir, ['edges.csv', 'nodes.csv'])
    action = exec_env.resolve_action({
        'pbs': 'bin/pbsrun_GRAPH.sh $SOURCE.abspath $TARGETS.abspath',
        'sge': 'bin/sgerun_GRAPH.sh $SOURCE.abspath $TARGETS.abspath',
        'local': 'bin/bamToEdges.py $SOURCE.abspath $TARGETS.abspath'
    })

    return 'edges', 'nodes', env.Command(targets, source, action)

Example #7

File: SConstruct_srmcl.py Project: thebevrishot/proxigenomics

def do_cluster(outdir, c):
    # TODO run over both weighted/unweighted?
    sources = [c['make_cluster_input']['nodemap'], c['do_cluster']['output']]
    target = appconfig.prepend_paths(outdir, config['cluster']['output'])

    action = exec_env.resolve_action({
        'pbs':
        'bin/metisClToMCL.py $SOURCES.abspath $TARGET.abspath'.format(c),
        'sge':
        'bin/metisClToMCL.py $SOURCES.abspath $TARGET.abspath'.format(c),
        'local':
        'bin/metisClToMCL.py $SOURCES.abspath $TARGET.abspath'.format(c)
    })

    return 'output', env.Command(target, sources, action)

Example #8

def do_cluster(outdir, c):
    # TODO run over both weighted/unweighted?
    source = c['make_cluster_input']['output']
    target = appconfig.prepend_paths(outdir, config['cluster']['output'])

    action = exec_env.resolve_action({
        'pbs':
        'bin/pbsrun_LOUVAIN.sh {0[otype]} $SOURCE.abspath $TARGET.abspath'.
        format(c),
        'sge':
        'bin/sgerun_LOUVAIN.sh {0[otype]} $SOURCE.abspath $TARGET.abspath'.
        format(c),
        'local':
        'bin/louvain.py --otype {0[otype]} $SOURCE.abspath $TARGET.abspath'.
        format(c)
    })

    return 'output', env.Command(target, source, action)

Example #9

File: SConstruct_srmcl.py Project: thebevrishot/proxigenomics

def make_cluster_input(outdir, c):

    sources = [str(c['make_graph']['edges']), str(c['make_graph']['nodes'])]
    base_out = appconfig.prepend_paths(outdir, config['cluster']['input'])[0]
    targets = [base_out, base_out + '.nodemap']

    action = exec_env.resolve_action({
        'pbs':
        'bin/pbsrun_MKMETIS.sh {0[ctg_minlen]} $SOURCES.abspath $TARGETS.abspath'
        .format(config),
        'sge':
        'bin/sgerun_MKMETIS.sh {0[ctg_minlen]} $SOURCES.abspath $TARGETS.abspath'
        .format(config),
        'local':
        'bin/edgeToMetis.py --fmt metis -m {0[ctg_minlen]} $SOURCES.abspath $TARGETS.abspath'
        .format(config)
    })

    return 'output', 'nodemap', env.Command(targets, sources, action)