shankara-a
commented
4 years ago Hi,
Could you please clarify your inputs. I am not sure what is in 'input.maf'.
Closed XuanYuXu closed 2 years ago
shankara-a
commented
4 years ago Hi,
Could you please clarify your inputs. I am not sure what is in 'input.maf'.
Angone can tell me why it happened?I do not what to do
In [10]: sa.run_maf('input.maf' , outdir='./ardnmf_output/', cosmic='cosmic2', hg_build='./ref/hg19.2bit', nruns=10)
Loading spectra from input.maf
ParserError Traceback (most recent call last)
C:\Anaconda3\lib\site-packages\signatureanalyzer\signatureanalyzer.py in run_maf(maf, outdir, cosmic, hg_build, nruns, verbose, plot_results, *nmf_kwargs) 83 print(" Loading spectra from {}".format(maf)) 84 maf, spectra = get_spectra_from_maf( ---> 85 pd.read_csv(maf, sep='\t'), 86 hgfile=hg_build, 87 cosmic=cosmic
C:\Anaconda3\lib\site-packages\pandas\io\parsers.py in parser_f(filepath_or_buffer, sep, delimiter, header, names, index_col, usecols, squeeze, prefix, mangle_dupe_cols, dtype, engine, converters, true_values, false_values, skipinitialspace, skiprows, skipfooter, nrows, na_values, keep_default_na, na_filter, verbose, skip_blank_lines, parse_dates, infer_datetime_format, keep_date_col, date_parser, dayfirst, cache_dates, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, doublequote, escapechar, comment, encoding, dialect, error_bad_lines, warn_bad_lines, delim_whitespace, low_memory, memory_map, float_precision) 674 ) 675 --> 676 return _read(filepath_or_buffer, kwds) 677 678 parser_f.name = name
C:\Anaconda3\lib\site-packages\pandas\io\parsers.py in _read(filepath_or_buffer, kwds) 452 453 try: --> 454 data = parser.read(nrows) 455 finally: 456 parser.close()
C:\Anaconda3\lib\site-packages\pandas\io\parsers.py in read(self, nrows) 1131 def read(self, nrows=None): 1132 nrows = _validate_integer("nrows", nrows) -> 1133 ret = self._engine.read(nrows) 1134 1135 # May alter columns / col_dict
C:\Anaconda3\lib\site-packages\pandas\io\parsers.py in read(self, nrows) 2035 def read(self, nrows=None): 2036 try: -> 2037 data = self._reader.read(nrows) 2038 except StopIteration: 2039 if self._first_chunk:
pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader.read()
pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._read_low_memory()
pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._read_rows()
pandas_libs\parsers.pyx in pandas._libs.parsers.TextReader._tokenize_rows()
pandas_libs\parsers.pyx in pandas._libs.parsers.raise_parser_error()
ParserError: Error tokenizing data. C error: Expected 1 fields in line 6, saw 120