for c in category_list:
c.out()
parser = argparse.ArgumentParser()
parser.add_argument(
'fusion_cluster_file',
action='store',
help=
'Fusion reannation file clustered by head/tail genes. (.reann.cluster file)'
)
parser.add_argument('outdir', action='store', help='outdir to write files to')
args = parser.parse_args()
cluster = args.fusion_cluster_file
outdir = args.outdir
category_stats = pygeneann.CategoryFusionStats(cluster)
fusion_list = category_stats.category_list
for i in range(2, 8):
filtered_list = filter(lambda x: len(x.tools) == i, fusion_list)
#print(i, len(filtered_list))
#if i == 5:
f = open(os.path.join(outdir, cluster + "." + str(i) + "CALLERS"), "w+")
sys.stdout = f
output_filtered_list(filtered_list)
f.close()
parser = argparse.ArgumentParser()
parser.add_argument('fusion_cluster_file',
action='store',
help='cluster file)')
parser.add_argument('--TP',
required=False,
action='store',
help='TP cluster file)')
args = parser.parse_args()
# len(sys.argv) will be 4 with TP file, and 2 without
#print(len(sys.argv))
category_stats = pygeneann.CategoryFusionStats(args.fusion_cluster_file)
fusion_list = category_stats.category_list
descending_fusion_list = []
# get number of tools
i = max([len(fusion.tools) for fusion in fusion_list])
#generate list sorted by tool number in descending order
while i > 0:
fusions_num_tools = filter_tools_num(fusion_list, i)
descending_fusion_list += fusions_num_tools
i -= 1
#output_filtered_list(descending_fusion_list)
if len(sys.argv) == 4:
category_stats_TP = pygeneann.CategoryFusionStats(args.TP)
fusion_list_TP = category_stats_TP.category_list
TP_FIDs = [fusion.fusion_IDs for fusion in fusion_list_TP]