Example #1
0
    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]