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0.8.8
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Zhuoqing Fang committed Nov 26, 2017
1 parent 617c816 commit 3e1e0b4
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4 changes: 1 addition & 3 deletions gseapy/__init__.py
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Expand Up @@ -3,6 +3,4 @@
from .enrichr import enrichr
from .parser import get_library_name

__version__='0.8.7'


__version__='0.8.8'
42 changes: 21 additions & 21 deletions gseapy/__main__.py
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Expand Up @@ -11,7 +11,7 @@
# or args = argparser.parse_args() will throw bugs!!!


__version__ = '0.8.7'
__version__ = '0.8.8'

def main():
"""The Main function/pipeline for GSEAPY."""
Expand All @@ -24,7 +24,7 @@ def main():
if subcommand == "replot":
# reproduce plots using GSEAPY
from .gsea import Replot
rep = Replot(indir=args.indir, outdir=args.outdir, weighted_score_type=args.weight,
rep = Replot(indir=args.indir, outdir=args.outdir, weighted_score_type=args.weight,
figsize=args.figsize, format=args.format, verbose=args.verbose)
rep.run()

Expand All @@ -33,15 +33,15 @@ def main():
# compute using GSEAPY
from .gsea import GSEA

gs = GSEA(args.data, args.gmt, args.cls, args.outdir,
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.seed, args.verbose)
gs.run()
elif subcommand == "prerank":
from .gsea import Prerank
pre = Prerank(args.rnk, args.gmt, args.outdir, args.label[0], args.label[1],

pre = Prerank(args.rnk, args.gmt, args.outdir, args.label[0], args.label[1],
args.mins, args.maxs, args.n, args.weight, args.ascending, args.threads,
args.figsize, args.format, args.graph, args.seed, args.verbose)
pre.run()
Expand All @@ -50,9 +50,9 @@ def main():
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, ascending=args.ascending,
processes=args.threads, figsize=args.figsize, format=args.format,
min_size=args.mins, max_size=args.maxs, permutation_num=args.n,
weighted_score_type=args.weight, ascending=args.ascending,
processes=args.threads, figsize=args.figsize, format=args.format,
graph_num=args.graph, seed=args.seed, verbose=args.verbose)
ss.run()

Expand All @@ -61,8 +61,8 @@ def main():
from .enrichr import Enrichr
enr = Enrichr(gene_list= args.gene_list, descriptions=args.descrip, gene_sets=args.library,
outdir=args.outdir, format=args.format, cutoff=args.thresh, figsize=args.figsize,
top_term=args.term, no_plot=args.no_plot, verbose=args.verbose)
enr.run()
top_term=args.term, no_plot=args.no_plot, verbose=args.verbose)
enr.run()
else:
argparser.print_help()
sys.exit(0)
Expand Down Expand Up @@ -125,7 +125,7 @@ def add_gsea_parser(subparsers):

# group for input files
group_input = argparser_gsea.add_argument_group("Input files arguments")
group_input.add_argument("-d", "--data", dest="data", action="store", type=str, required=True,
group_input.add_argument("-d", "--data", dest="data", action="store", type=str, required=True,
help="Input gene expression dataset file in txt format.Same with GSEA.")
group_input.add_argument("-c", "--cls", dest="cls", action="store", type=str, required=True,
help="Input class vector (phenotype) file in CLS format. Same with GSEA.")
Expand Down Expand Up @@ -165,17 +165,17 @@ def add_gsea_parser(subparsers):
help="Number of Processes you are going to use. Default: 1")

return

def add_prerank_parser(subparsers):
"""Add function 'prerank' argument parsers."""

argparser_prerank = subparsers.add_parser("prerank", help="Run GSEApy Prerank tool on preranked gene list.")

# group for input files
prerank_input = argparser_prerank.add_argument_group("Input files arguments")
prerank_input.add_argument("-r", "--rnk", dest="rnk", action="store", type=str, required=True,
prerank_input.add_argument("-r", "--rnk", dest="rnk", action="store", type=str, required=True,
help="ranking dataset file in .rnk format.Same with GSEA.")
prerank_input.add_argument("-g", "--gmt", dest="gmt", action="store", type=str, required=True,
prerank_input.add_argument("-g", "--gmt", dest="gmt", action="store", type=str, required=True,
help="Gene set database in GMT format. Same with GSEA.")
prerank_input.add_argument("-l", "--label", action='store', nargs=2, dest='label',
metavar=('pos', 'neg'), type=str, default=('Pos','Neg'),
Expand Down Expand Up @@ -203,7 +203,7 @@ def add_prerank_parser(subparsers):
help="Number of random seed. Default: None")
prerank_opt.add_argument("-p", "--threads", dest = "threads", action="store", type=int, default=1, metavar='procs',
help="Number of Processes you are going to use. Default: 1")

return

def add_singlesample_parser(subparsers):
Expand All @@ -213,7 +213,7 @@ def add_singlesample_parser(subparsers):

# group for input files
group_input = argparser_gsea.add_argument_group("Input files arguments")
group_input.add_argument("-d", "--data", dest="data", action="store", type=str, required=True,
group_input.add_argument("-d", "--data", dest="data", action="store", type=str, required=True,
help="Input gene expression dataset file in txt format. Same with GSEA.")
group_input.add_argument("-g", "--gmt", dest="gmt", action="store", type=str, required=True,
help="Gene set database in GMT format. Same with GSEA.")
Expand All @@ -224,7 +224,7 @@ def add_singlesample_parser(subparsers):
# group for General options.
group_opt = argparser_gsea.add_argument_group("GSEA advanced arguments")
group_opt.add_argument("--norm-method", dest = "norm", action="store", type=str,
default='rank', metavar='normalize',
default='rank', metavar='normalize',
choices=("rank", "log", "log_rank", "custom"),
help="Sample normalization method. Choose from {'rank', 'log', 'log_rank','custom'}. Default: rank")
group_opt.add_argument("-n", "--permu-num", dest = "n", action="store", type=int, default=1000, metavar='perNum',
Expand Down Expand Up @@ -264,7 +264,7 @@ def add_plot_parser(subparsers):
return
def add_enrichr_parser(subparsers):
"""Add function 'enrichr' argument parsers."""

argparser_enrichr = subparsers.add_parser("enrichr", help="Using enrichr API to perform GO analysis.")

# group for required options.
Expand All @@ -275,14 +275,14 @@ def add_enrichr_parser(subparsers):
help="Enrichr library name required. see online tool for libary names.")
enrichr_opt.add_argument("--description", action="store", dest="descrip", type=str, default='enrichr', metavar='strings',
help="It is recommended to enter a short description for your list so that multiple lists \
can be differentiated from each other if you choose to save or share your list.")
can be differentiated from each other if you choose to save or share your list.")
enrichr_opt.add_argument("--cut-off", action="store", dest="thresh", metavar='float', type=float, default=0.05,
help="Adjust-Pval cutoff, used for generating plots. Default: 0.05.")
enrichr_opt.add_argument("-t", "--top-term", dest="term", action="store", type=int, default=10, metavar='int',
help="Numbers of top terms showed in the plot. Default: 10")
#enrichr_opt.add_argument("--scale", dest = "scale", action="store", type=float, default=0.5, metavar='float',
# help="scatter dot scale in the dotplot. Default: 0.5")
enrichr_opt.add_argument("--no-plot", action='store_true', dest='no_plot', default=False,
# help="scatter dot scale in the dotplot. Default: 0.5")
enrichr_opt.add_argument("--no-plot", action='store_true', dest='no_plot', default=False,
help="Suppress the plot output.This is useful only if data are intrested. Default: False.")


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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -5,7 +5,7 @@



__version__='0.8.7'
__version__='0.8.8'

if sys.argv[-1] == 'publish':
os.system("python setup.py sdist bdist_wheel register upload")
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