sceps_sim/sim_utils.py at master · Genentech/sceps_sim · GitHub

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import argparse, logging, gzip, os
import scanpy as sc
import pandas as pd
import numpy as np

logging.basicConfig(level=logging.INFO, format='%(asctime)s - %(levelname)s - %(message)s')

MIN_NUM_CELL = 5
MIN_NUM_DONOR = 30
EPS = 1e-16
ERROR_TOL = 1e-3

def get_command_line_sim():

    # Create the parser
    parser = argparse.ArgumentParser(description="Generate simulated data")

    # Add the arguments
    parser.add_argument('--adata', type=str, required=False,
                        help='scRNA-seq data')

    parser.add_argument('--cell-type-col', type=str, required=False, default='',
                        help='Cell type column name')

    parser.add_argument('--gene-id-col', type=str, required=False, default='ID',
                        help='Column name for gene ID')

    parser.add_argument('--cell-id-col', type=str, required=False, default='ID',
                        help='Column name for gene ID')

    parser.add_argument('--focal-cell-type', type=str, required=False, default='',
                        help='Cell type to focus on')

    parser.add_argument('--donor-id-col', type=str, required=False,
                        help='Donor ID column name')

    parser.add_argument('--gene-list', type=str, required=False, default='',
                        help='A list of genes of interest')

    parser.add_argument('--max-step-size', type=int, required=False, default=15,
                        help='Max number of step size in the random walk')

    parser.add_argument('--num-gwas-genes', type=int, required=False, default=1000,
                        help='Number of gwas genes to select')

    parser.add_argument('--prob-thres', type=float, required=False, default=0.0,
                        help='Random walk probability threshold')

    parser.add_argument('--min-expr-var-thres', type=float, required=False, default=1e-4,
                        help='Gene expression standard deviation threshold')

    parser.add_argument('--max-expr-var-thres', type=float, required=False, default=10.0,
                        help='Gene expression standard deviation threshold')

    parser.add_argument('--prop-causal-cells', type=float, required=False, default=0.05,
                        help='Proportion of causal cell neighborhoods')

    parser.add_argument('--num-expr-bins', type=int, required=False, default=10,
                        help='Number of bins on the mean expression')

    parser.add_argument('--prop-causal-gwas-genes', type=float, required=False, default=0.5,
                        help='Proportion of causal genes')

    parser.add_argument('--varexp-total', type=float, required=False, default=0.3,
                        help='variance in outcome explained by GWAS genes')

    parser.add_argument('--varexp-per-gwas-gene', type=float, required=False, default=0.3,
                        help='variance in outcome explained by GWAS genes')

    parser.add_argument('--varexp-per-control-gene', type=float, required=False, default=0.3,
                        help='variance in outcome explained by GWAS genes')

    parser.add_argument('--max-relmat-gwas-ctrl-corr', type=float, required=False, default=0.95,
                        help='variance in outcome explained by all the genes')

    parser.add_argument('--gwas-causal-enrichment', type=float, required=False, default=10.0,
                        help='Enrichment of causal genes among GWAS genes')

    parser.add_argument('--num-sim', type=int, required=False, default=2000,
                        help='Number of simulations')

    parser.add_argument('--min-num-donor', type=int, required=False, default=30,
                        help='Minimum number of donors in each neighborhood')

    parser.add_argument('--min-num-cell', type=int, required=False, default=5,
                        help='Minimum number of cell in each neighborhood')

    parser.add_argument('--neighborhood-definition-method', type=str, required=False, default='nam',
                        help='Choose from threshold or nam')

    parser.add_argument('--seed', type=int, required=True, help="Seed for the random number generator")

    parser.add_argument('--out-dir', type=str, required=False,
                        help='Output directory')

    # Execute the parse_args() method
    args = parser.parse_args()

    return args


def get_sim_str(args):

    out_str = 'numgwasgenes{}'.format(args.num_gwas_genes)
    out_str = out_str + '_propcaugwasgenes{}'.format(args.prop_causal_gwas_genes)
    out_str = out_str + '_gwascauen{}'.format(args.gwas_causal_enrichment)
    out_str = out_str + '_varexptotal{}'.format(args.varexp_total)
    out_str = out_str + '_varexppergwasgene{}'.format(args.varexp_per_gwas_gene)
    out_str = out_str + '_varexppercontrolgene{}'.format(args.varexp_per_control_gene)

    return out_str