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def main():
"""The Main function/pipeline for GSEApy."""
# Parse options...
argparser = prepare_argparser()
args = argparser.parse_args()
subcommand = args.subcommand_name
if subcommand == "replot":
# reproduce plots using GSEAPY
from .gsea import Replot
rep = Replot(indir=args.indir, outdir=args.outdir, weighted_score_type=args.weight,
figsize=args.figsize, graph_num=args.graph,
format=args.format, verbose=args.verbose)
rep.run()
elif subcommand == "gsea":
# compute using GSEAPY
from .gsea import GSEA
gs = GSEA(args.data, args.gmt, args.cls, args.outdir,
args.mins, args.maxs, args.n, args.weight,
args.type, args.method, args.ascending, args.threads,
args.figsize, args.format, args.graph, args.noplot, args.seed, args.verbose)
gs.run()
elif subcommand == "prerank":
from .gsea import Prerank
:param indir: GSEA desktop results directory. In the sub folder, you must contain edb file folder.
:param outdir: Output directory.
:param float weighted_score_type: weighted score type. choose from {0,1,1.5,2}. Default: 1.
:param list figsize: Matplotlib output figure figsize. Default: [6.5,6].
:param str format: Matplotlib output figure format. Default: 'pdf'.
:param int min_size: Min size of input genes presented in Gene Sets. Default: 3.
:param int max_size: Max size of input genes presented in Gene Sets. Default: 5000.
You are not encouraged to use min_size, or max_size argument in :func:`replot` function.
Because gmt file has already been filtered.
:param verbose: Bool, increase output verbosity, print out progress of your job, Default: False.
:return: Generate new figures with selected figure format. Default: 'pdf'.
"""
rep = Replot(indir, outdir, weighted_score_type,
min_size, max_size, figsize, graph_num, format, verbose)
rep.run()
return