def setup_dirs(data):
    """ sets up directories for step3 data """
    ## make output folder for clusters
    pdir = os.path.realpath(data.paramsdict["project_dir"])
    data.dirs.clusts = os.path.join(pdir, "{}_clust_{}"\
                       .format(data.name, data.paramsdict["clust_threshold"]))
    if not os.path.exists(data.dirs.clusts):
        os.mkdir(data.dirs.clusts)

    ## make a tmpdir for align files
    data.tmpdir = os.path.abspath(os.path.expanduser(
        os.path.join(pdir, data.name+'-tmpalign')))
    if not os.path.exists(data.tmpdir):
        os.mkdir(data.tmpdir)

    ## If ref mapping, init samples and make the refmapping output directory.
    if not data.paramsdict["assembly_method"] == "denovo":
        ## make output directory for read mapping process
        data.dirs.refmapping = os.path.join(pdir, "{}_refmapping".format(data.name))
        if not os.path.exists(data.dirs.refmapping):
            os.mkdir(data.dirs.refmapping)
def setup_dirs(data):
    """ sets up directories for step3 data """
    ## make output folder for clusters
    pdir = os.path.realpath(data.paramsdict["project_dir"])
    data.dirs.clusts = os.path.join(pdir, "{}_clust_{}"\
                       .format(data.name, data.paramsdict["clust_threshold"]))
    if not os.path.exists(data.dirs.clusts):
        os.mkdir(data.dirs.clusts)

    ## make a tmpdir for align files
    data.tmpdir = os.path.abspath(os.path.expanduser(
        os.path.join(pdir, data.name+'-tmpalign')))
    if not os.path.exists(data.tmpdir):
        os.mkdir(data.tmpdir)

    ## If ref mapping, init samples and make the refmapping output directory.
    if not data.paramsdict["assembly_method"] == "denovo":
        ## make output directory for read mapping process
        data.dirs.refmapping = os.path.join(pdir, "{}_refmapping".format(data.name))
        if not os.path.exists(data.dirs.refmapping):
            os.mkdir(data.dirs.refmapping)
def setup_dirs ( data ) : ## make output folder for clusters pdir = os . path . realpath ( data . paramsdict [ "project_dir" ] ) data . dirs . clusts = os . path . join ( pdir , "{}_clust_{}" . format ( data . name , data . paramsdict [ "clust_threshold" ] ) ) if not os . path . exists ( data . dirs . clusts ) : os . mkdir ( data . dirs . clusts ) ## make a tmpdir for align files data . tmpdir = os . path . abspath ( os . path . expanduser ( os . path . join ( pdir , data . name + '-tmpalign' ) ) ) if not os . path . exists ( data . tmpdir ) : os . mkdir ( data . tmpdir ) ## If ref mapping, init samples and make the refmapping output directory. if not data . paramsdict [ "assembly_method" ] == "denovo" : ## make output directory for read mapping process data . dirs . refmapping = os . path . join ( pdir , "{}_refmapping" . format ( data . name ) ) if not os . path . exists ( data . dirs . refmapping ) : os . mkdir ( data . dirs . refmapping )
sets up directories for step3 data
sets up directories for step3 data