Closed tstannius closed 5 years ago
cellex.utils.mapping.ens_mouse_to_ens_human(eso.results["esmu"], drop_unmapped=True, verbose=True)
Map gene names
Mapping: mouse ensembl gene id's --> human ensembl gene id's ... --------------------------------------------------------------------------- FileNotFoundError Traceback (most recent call last) <ipython-input-11-75787d394ce1> in <module> ----> 1 cellex.utils.mapping.ens_mouse_to_ens_human(eso.results["esmu"], drop_unmapped=True, verbose=True) /tools/anaconda/envs/djw472/py3_PT/lib/python3.7/site-packages/cellex/utils/mapping/ens_mouse_to_ens_human.py in ens_mouse_to_ens_human(df_unmapped, drop_unmapped, verbose) 35 fp_mapping_file = "CELLEX/cellex/utils/mapping/maps/hsapiens_mmusculus_unique_orthologs.GRCh37.ens_v91.txt.gz" 36 ---> 37 df_map = pd.read_csv(fp_mapping_file, delim_whitespace=True) 38 39 # create dictionary for mapping mouse ensemble gene id's to human ensembl gene id's /tools/anaconda/envs/djw472/py3_PT/lib/python3.7/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) 683 ) 684 --> 685 return _read(filepath_or_buffer, kwds) 686 687 parser_f.__name__ = name /tools/anaconda/envs/djw472/py3_PT/lib/python3.7/site-packages/pandas/io/parsers.py in _read(filepath_or_buffer, kwds) 455 456 # Create the parser. --> 457 parser = TextFileReader(fp_or_buf, **kwds) 458 459 if chunksize or iterator: /tools/anaconda/envs/djw472/py3_PT/lib/python3.7/site-packages/pandas/io/parsers.py in __init__(self, f, engine, **kwds) 893 self.options["has_index_names"] = kwds["has_index_names"] 894 --> 895 self._make_engine(self.engine) 896 897 def close(self): /tools/anaconda/envs/djw472/py3_PT/lib/python3.7/site-packages/pandas/io/parsers.py in _make_engine(self, engine) 1133 def _make_engine(self, engine="c"): 1134 if engine == "c": -> 1135 self._engine = CParserWrapper(self.f, **self.options) 1136 else: 1137 if engine == "python": /tools/anaconda/envs/djw472/py3_PT/lib/python3.7/site-packages/pandas/io/parsers.py in __init__(self, src, **kwds) 1904 kwds["usecols"] = self.usecols 1905 -> 1906 self._reader = parsers.TextReader(src, **kwds) 1907 self.unnamed_cols = self._reader.unnamed_cols 1908 pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader.__cinit__() pandas/_libs/parsers.pyx in pandas._libs.parsers.TextReader._setup_parser_source() /tools/anaconda/envs/djw472/py3_PT/lib/python3.7/gzip.py in __init__(self, filename, mode, compresslevel, fileobj, mtime) 161 mode += 'b' 162 if fileobj is None: --> 163 fileobj = self.myfileobj = builtins.open(filename, mode or 'rb') 164 if filename is None: 165 filename = getattr(fileobj, 'name', '') FileNotFoundError: [Errno 2] No such file or directory: 'CELLEX/cellex/utils/mapping/maps/hsapiens_mmusculus_unique_orthologs.GRCh37.ens_v91.txt.gz'
Fixed by @pvtodorov in #6
tstannius
commented
5 years ago tstannius
commented
5 years ago
code entered
expected behavior
Map gene names
actual behavior