dtype={c: str for c in cols_shared})
except (pd.parser.CParserError, csv.Error) as err:
raise ValueError("Unexpected dataframe contents:\n%s\n%s" %
(line, next(infile)))
// Calculate values for output columns
if exons:
After Change
cols_rest = ["_start_tx", "_end_tx", // Transcription
"_start_cds", "_end_cds", // Coding region
"_exon_count", "exon_starts", "exon_ends"]
converters = {"exon_starts": _split_commas, "exon_ends": _split_commas}
elif cds:
// Use CDS instead of transcription region
cols_rest = ["_start_tx", "_end_tx",
"start", "end",
"_exon_count", "_exon_starts", "_exon_ends"]
else:
cols_rest = ["start", "end",
"_start_cds", "_end_cds",
"_exon_count", "_exon_starts", "_exon_ends"]
colnames = cols_shared + cols_rest
usecols = [c for c in colnames if not c.startswith("_")]
// Parse the file contents
dframe = pd.read_table(infile, header=None, na_filter=False,
names=colnames, usecols=usecols,
dtype={c: str for c in cols_shared},
converters=converters)
// Calculate values for output columns
if exons:
dframe = pd.DataFrame.from_records(_split_exons(dframe),
columns=cols_shared + ["start", "end"])
dframe["start"] = dframe["start"].astype("int")
dframe["end"] = dframe["end"].astype("int")
return (dframe.assign(start=dframe.start - 1)
.sort_values(["chromosome", "start", "end"])
.reset_index(drop=True))
