cytophenograph.v6.py

import optparse
from PhenoFunctions_v6 import *
import traceback

parser = optparse.OptionParser(usage='python ./Cytophenograph/cytophenograph.v5.py -i $abs_path/Cytophenograph/Test_dataset/CD8_Panel_II_channelvalues_GA_downSampled/ -o $abs_path/Cytophenograph/output_test -k 300 -m $abs_path/Cytophenograph/Test_dataset/CD8_bulk_markers_to_exclude.txt -n Test -t 10 -p $abs_path/Cytophenograph/Test_dataset/Info_file_bulk_Test.xlsx -c VIA', version='5.0')
parser.add_option('-a', action="store_true", dest="arcsin", default=False,
                  help='Perform arcsinh transformation on data.')
parser.add_option('-b', action="store_true", dest="batch", default=False,
                  help='Perform batch correction with Scanorama.')
parser.add_option('-c', type='choice', choices=['Phenograph', 'VIA', 'FlowSOM'],
                  dest="clustering",
                  default="Phenograph", help='Tool selecting for clustering, Selection available are [Phenograph, VIA, FlowSOM].')
parser.add_option('-d', action="store", dest="mindist", default=0.5, type=float, help='min_dist parameter for UMAP generation')
parser.add_option('-e', type='choice', choices=['Sample', 'Cell_type','ID', 'EXP', 'Time_point', 'Condition'],
                  dest="batchcov",
                  default="Sample", help='Please, specify covariate to correct with Scanorama')
parser.add_option('-f', type='choice', choices=['All', 'Balanced', 'Fixed'],
                  dest="downsampling",
                  default="All", help='Concatenation Method. Available options are All, Balanced, Fixed.')
parser.add_option('-g', action="store", dest="cellnumber", default=1000, type=int, help='Number of event to for downsampling.')
parser.add_option('-i', action="store", dest="input_folder", help='Absolute path of folder with CSV files.')
parser.add_option('-k', action="store", dest="kmeancoef", help='Number for nearest neighbors search for Phenograph execution.Deafult value is 30',
                  type='string', default='30')
parser.add_option('-l', action="store",
                  dest="fileformat", help='Flag to change option format. Default: CSV', choices=['CSV', 'FCS'],
                  type='choice', default='CSV')
parser.add_option('-m', action="store", dest="markerlist", help='Text file with features(channel name) to exclude during clustering execution.')
parser.add_option('-n', action="store", dest="analysis_name", help='Analysis name.')
parser.add_option('-o', action="store", dest="output_folder", help='Absolute path of output folder. TIPS: Please use an empty folder.')
parser.add_option('-p', action="store", dest="pheno", default="Condition",
                  help='Excel file with the following columns "Sample-Cell_type-EXP-ID-Time_point-Condition-Count", that will be integrated as metadata.')
parser.add_option('-r', type='choice', choices=['Full', 'UMAP', 'Clustering'],
                  dest="runtime",
                  default="Full", help='Runtime option for custom analysis. The available options are Full, UMAP, Clustering.')
parser.add_option('-s', action="store", dest="spread", default=1.0, type=float, help='spread parameter for UMAP generation')
parser.add_option('-t', action="store", dest="thread", type=int, default=1, help='Number of jobs.')
parser.add_option('-w', action="store", dest="knn", help='Number of K-Nearest Neighbors for VIA KNN graph. Min allowed value is 5, Max allowed value is 100. Deafult value is 30',
                  type=int, default=30)
parser.add_option('-y', action="store", dest="maxclus", help='Exact number of clusters for meta-clustering. Max allowed value is 31.',
                  type=int, default=31)
parser.add_option('-z', action="store", dest="resolution", help='A parameter value controlling the coarseness of the VIA clustering. Min allowed value is 0.2, Max allowed value is 1.5. Deafult value is 1.0',
                  type=float, default=1.0)

options, args = parser.parse_args()


if __name__ == '__main__':
    DictInfo = dict()

    run = Cytophenograph(info_file=options.pheno,
                         input_folder=options.input_folder,
                         output_folder=options.output_folder,
                         k_coef=options.kmeancoef,
                         marker_list=options.markerlist,
                         analysis_name=options.analysis_name,
                         thread=int(options.thread),
                         tool=options.clustering,
                         batch=options.batch,
                         batchcov=options.batchcov,
                         mindist=options.mindist,
                         spread=options.spread,
                         runtime=options.runtime,
                         knn=options.knn,
                         resolution=options.resolution,
                         maxclus=options.maxclus,
                         downsampling=options.downsampling,
                         cellnumber=options.cellnumber,
                         filetype=options.fileformat,
                         arcsinh=options.arcsin)
    try:
        DictInfo["Infofile"] = run.read_info_file()
        DictInfo["List_csv_files"] = run.import_all_event()
        DictInfo["adata_conc"] = run.concatenate_dataframe(DictInfo["Infofile"],
                                                           DictInfo["List_csv_files"])
        DictInfo["pathmarkerfile"], DictInfo["basenamemarkerfilepath"] = run.loadmarkers()
        DictInfo["markertoexclude"] = run.checkmarkers()
        DictInfo["markertoinclude"] = run.splitmarker()
        if options.runtime != 'UMAP':
            if options.clustering == "Phenograph":
                DictInfo["phenograph_adata"] = run.runphenograph()
            elif options.clustering == "VIA":
                DictInfo["via_adata"] = run.runvia()
            elif options.clustering == "FlowSOM":
                DictInfo["flowsom_adata"] = run.runflowsom()
            run.groupbycluster()
            run.groupbysample()
            run.exporting()
        if options.runtime == 'UMAP':
            run.runtimeumap()
            run.groupbysample()
            run.exporting()
    except Exception:
        print(traceback.format_exc())
        run.log.error("Execution Error!")
        sys.exit(1)