dc682236d6f167f733d65057c4faa07a20e32d04,bipy/core/distance.py,DistanceMatrix,from_file,#Any#Any#Any#,25

Before Change

            if line_idx < num_sids:
                if tokens[0] == sids[line_idx]:
                    row_data = map(float, tokens[1:])

                    if len(row_data) == num_sids:
                        data[line_idx, :] = row_data
                    else:
                        raise InvalidDistanceMatrixFormatError("The number of "
                                "values in row number %d doesn"t match the "
                                "number of sample IDs in the header." %
                                line_idx + 1)
                else:
                    raise SampleIdMismatchError("Encountered mismatched "
                            "sample IDs while parsing the distance matrix "
                            "file. Please ensure the sample IDs match between "

After Change

        for line_idx, line in enumerate(dm_f):
            tokens = map(lambda e: e.strip(), line.strip().split(delimiter))

            if line_idx == 0:
                // We"re at the header (sample IDs).
                sids = tokens
                num_sids = len(sids)
                data = np.empty((num_sids, num_sids))
            elif line_idx <= num_sids:
                if len(tokens) != num_sids + 1:
                    raise DistanceMatrixFormatError("The number of values in "
                            "row number %d is not equal to the number of "
                            "sample IDs in the header." % line_idx)

                row_idx = line_idx - 1

                if tokens[0] == sids[row_idx]:
                    row_data = np.zeros(num_sids)

                    for col_idx in range(row_idx):
                        row_data[col_idx] = float(tokens[col_idx + 1])

                    data[row_idx,:] = row_data
                else:
                    raise SampleIDMismatchError("Encountered mismatched "
                            "sample IDs while parsing the distance matrix "
                            "file. Please ensure the sample IDs match between "
                            "the distance matrix header (first row) and the "
                            "row labels (first column).")
            else:
                if "".join(tokens):
                    // If it isn"t a blank line, raise an error because we
                    // shouldn"t ignore extra data.
                    raise InvalidDistanceMatrixFormatError("Encountered extra "
                            "rows without corresponding sample IDs in the "
                            "header.")

        if sids is None:
            raise MissingHeaderError("Could not find a header line containing "
                    "sample IDs in the distance matrix file. Is the file "
                    "empty?")

Instances