Hi,
I'm trying to run cocacola.py, but I get an error just after running it.
python /services/tools/cocacola-python/20170305/cocacola.py --contig_file contig.fa --abundance_profiles depth.cov --composition_profiles kmer_4_tmp.csv --edge_list linkage.tsv --output result_cocacola.csv
When running python 2, I get this error:
Traceback (most recent call last):
File "/services/tools/cocacola-python/20170305/cocacola.py", line 180, in
edgelist = pd.DataFrame(np.genfromtxt(args.edge_list, dtype=str, converters={0: lambda s: mapObj[s], 1: lambda s: mapObj[s], 2: lambda s: float(s)})).as_matrix()
File "/services/tools/anaconda-2.2.0/lib/python2.7/site-packages/numpy/lib/npyio.py", line 1778, in genfromtxt
missing_values=missing_values[i],)
File "/services/tools/anaconda-2.2.0/lib/python2.7/site-packages/numpy/lib/_iotools.py", line 841, in update
tester = func(testing_value or b'1')
File "/services/tools/cocacola-python/20170305/cocacola.py", line 180, in
edgelist = pd.DataFrame(np.genfromtxt(args.edge_list, dtype=str, converters={0: lambda s: mapObj[s], 1: lambda s: mapObj[s], 2: lambda s: float(s)})).as_matrix()
KeyError: 'contig1'
If running python3, I get same error:
Traceback (most recent call last):
File "/services/tools/cocacola-python/20170305/cocacola.py", line 180, in
edgelist = pd.DataFrame(np.genfromtxt(args.edge_list, dtype=str, converters={0: lambda s: mapObj[s], 1: lambda s: mapObj[s], 2: lambda s: float(s)})).as_matrix()
File "/services/tools/anaconda3/4.4.0/lib/python3.6/site-packages/numpy/lib/npyio.py", line 1778, in genfromtxt
missing_values=missing_values[i],)
File "/services/tools/anaconda3/4.4.0/lib/python3.6/site-packages/numpy/lib/_iotools.py", line 841, in update
tester = func(testing_value or b'1')
File "/services/tools/cocacola-python/20170305/cocacola.py", line 180, in
edgelist = pd.DataFrame(np.genfromtxt(args.edge_list, dtype=str, converters={0: lambda s: mapObj[s], 1: lambda s: mapObj[s], 2: lambda s: float(s)})).as_matrix()
KeyError: b'contig1'
Any idea about what is going on?
Thanks in advance.