I need to get data from the "matrix matrix file (s)" file, which is here , but errors occur when reading it with read_csv. Help me to understand.

Here are the errors:

--------------------------------------------------------------------------- CParserError Traceback (most recent call last) <ipython-input-29-6d3982f93f22> in <module>() ----> 1 pd.read_csv("GSE7670_series_matrix.txt") /usr/local/lib/python3.4/dist-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, iterator, chunksize, compression, thousands, decimal, lineterminator, quotechar, quoting, escapechar, comment, encoding, dialect, tupleize_cols, error_bad_lines, warn_bad_lines, skip_footer, doublequote, delim_whitespace, as_recarray, compact_ints, use_unsigned, low_memory, buffer_lines, memory_map, float_precision) 560 skip_blank_lines=skip_blank_lines) 561 --> 562 return _read(filepath_or_buffer, kwds) 563 564 parser_f.__name__ = name /usr/local/lib/python3.4/dist-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds) 323 return parser 324 --> 325 return parser.read() 326 327 _parser_defaults = { /usr/local/lib/python3.4/dist-packages/pandas/io/parsers.py in read(self, nrows) 813 raise ValueError('skip_footer not supported for iteration') 814 --> 815 ret = self._engine.read(nrows) 816 817 if self.options.get('as_recarray'): /usr/local/lib/python3.4/dist-packages/pandas/io/parsers.py in read(self, nrows) 1312 def read(self, nrows=None): 1313 try: -> 1314 data = self._reader.read(nrows) 1315 except StopIteration: 1316 if self._first_chunk: pandas/parser.pyx in pandas.parser.TextReader.read (pandas/parser.c:8748)() pandas/parser.pyx in pandas.parser.TextReader._read_low_memory (pandas/parser.c:9003)() pandas/parser.pyx in pandas.parser.TextReader._read_rows (pandas/parser.c:9731)() pandas/parser.pyx in pandas.parser.TextReader._tokenize_rows (pandas/parser.c:9602)() pandas/parser.pyx in pandas.parser.raise_parser_error (pandas/parser.c:23325)() CParserError: Error tokenizing data. C error: Expected 1 fields in line 7, saw 10

    1 answer 1

    I think you are not quite reading this file.

    CParserError: Error tokenizing data. C error: Expected 1 fields in line 7, saw 10

    says that Pandas saw 10 fields in line 7, and expected to see only one field.

    try the following:

     fn = r'/path/to/file.csv' df = pd.read_csv(fn, skiprows=70, sep='\s*')

    PS I do not have access to your file, so I tested my solution on this file, in which the first 70 lines are a description. Change 70 to the number of lines of description in your file.

    • Thanks, it helped. - Tolkachev Ivan