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elif subcommand == "ssgsea":
from .gsea import SingleSampleGSEA
ss = SingleSampleGSEA(data=args.data, gene_sets=args.gmt, outdir=args.outdir,
sample_norm_method=args.norm,
min_size=args.mins, max_size=args.maxs, permutation_num=args.n,
weighted_score_type=args.weight, scale=args.scale,
ascending=args.ascending, processes=args.threads,
figsize=args.figsize, format=args.format, graph_num=args.graph,
no_plot=args.noplot, seed=args.seed, verbose=args.verbose)
ss.run()
elif subcommand == "enrichr":
# calling enrichr API
from .enrichr import Enrichr
enr = Enrichr(gene_list=args.gene_list, descriptions=args.descrip,
gene_sets=args.library, organism=args.organism,
outdir=args.outdir, format=args.format, cutoff=args.thresh,
background=args.bg, figsize=args.figsize,
top_term=args.term, no_plot=args.noplot, verbose=args.verbose)
enr.run()
elif subcommand == "biomart":
from .parser import Biomart
# read input file or a argument
name, value = args.filter
if os.path.isfile(value):
with open(value, 'r') as val:
lines = val.readlines()
value = [ l.strip() for l in lines]
# run query
bm = Biomart(host=args.host, verbose=args.verbose)
bm.query(dataset=args.bg, attributes=args.attrs.split(","),
>>> from gseapy.parser import Biomart
>>> bm = Biomart(verbose=False, host="asia.ensembl.org")
>>> ## view validated marts
>>> marts = bm.get_marts()
>>> ## view validated dataset
>>> datasets = bm.get_datasets(mart='ENSEMBL_MART_ENSEMBL')
:param str format: Output figure format supported by matplotlib,('pdf','png','eps'...). Default: 'pdf'.
:param list figsize: Matplotlib figsize, accept a tuple or list, e.g. (width,height). Default: (6.5,6).
:param bool no_plot: If equals to True, no figure will be drawn. Default: False.
:param bool verbose: Increase output verbosity, print out progress of your job, Default: False.
:return: An Enrichr object, which obj.res2d stores your last query, obj.results stores your all queries.
"""
enr = Enrichr(gene_list, gene_sets, organism, description, outdir,
cutoff, background, format, figsize, top_term, no_plot, verbose)
enr.run()
return enr