scpathoquant

#!/usr/bin/env python

__author__ = "Leanne Whitmore"
__email__ = "leanne382@gmail.com"
__description__ = "Quantifies single cell pathogen derived reads"

# ----Libraries
import os
import argparse
import shutil
from spq.map_reads import process_reads as pr
from spq.map_reads import map_reads as mr
from spq.process_10x import extract10x as ex
from spq.quantify import patho_copies as vc
from spq.quantify import patho_genes as vg
from spq.quantify import integrate
from spq.visualization import viz


def parse_arguments():
    parser = argparse.ArgumentParser(prog="scPathoQuant", description="Quantify sc viral/bacterial mapping reads")
    parser.add_argument("-10x", "--path10x", type=str, required=True)
    parser.add_argument("-op", "--output_path", default="output_scPathoQuant")
    parser.add_argument("-p", "--processors", default=1)
    parser.add_argument("-p2genome", "--path2genome", type=str, required=True)
    parser.add_argument("-align", "--aligner", type=str, default="bbmap")
    parser.add_argument("-v", "--vizualization", type=str, default="True")
    parser.add_argument("-c", "--coveragemaps", type=str, default="True")
    parser.add_argument("-in_filtered", "--input_filtered_folder", type=str, required=False, default="filtered_feature_bc_matrix")
    parser.add_argument("-out_filtered", "--output_filtered_folder", type=str, required=False, default="filtered_feature_bc_matrix")
    parser.add_argument("-in_raw", "--input_raw_folder", type=str, required=False, default="raw_feature_bc_matrix")
    parser.add_argument("-out_raw", "--output_raw_folder", type=str, required=False, default="raw_feature_bc_matrix")
    parser.add_argument("--tmp_removal", required=False, action="store_true")
    parser.add_argument("--bbmap_params",  nargs="+")
    parser.add_argument("--bowtie2_params", nargs="+")

    return parser.parse_args()

if __name__ == '__main__':
    args = parse_arguments()
    ex.checkgenomefile(args)
    viable_cb = ex.extract_viable_10x(args.path10x)
    pr.process_unmapped_reads(args, viable_cb)
    mr.map2pathogengenome(args)
    dfvc, virus_names = vc.htseq_run(args)
    if args.vizualization=="True":
        viz.generate_viral_copy_plots(args, dfvc)
        if args.coveragemaps=="True":
            viz.generate_coverage_maps(args, dfvc)
    integrate.integrate_data_2_matrix(args, dfvc, virus_names)
    dfgenes = vg.htseq_run(args, virus_names)
    if dfgenes is not False:
        if args.vizualization=="True":
            viz.generate_viral_gene_plots(args, dfgenes)
        integrate.integrate_pathogenes_data_2_matrix(args, dfgenes)
    if args.tmp_removal:
        shutil.rmtree(os.path.join(args.output_path,"_tmp"))