However, the belowe code caused the following errors:
Traceback (most recent call last):
File "/anaconda/envs/bioinf-scripts/lib/python3.7/site-packages/gtfparse/read_gtf.py", line 103, in parse_gtf
for df in chunk_iterator:
File "/anaconda/envs/bioinf-scripts/lib/python3.7/site-packages/pandas/io/parsers.py", line 1128, in __next__
return self.get_chunk()
File "/anaconda/envs/bioinf-scripts/lib/python3.7/site-packages/pandas/io/parsers.py", line 1188, in get_chunk
return self.read(nrows=size)
File "/anaconda/envs/bioinf-scripts/lib/python3.7/site-packages/pandas/io/parsers.py", line 1154, in read
ret = self._engine.read(nrows)
File "/anaconda/envs/bioinf-scripts/lib/python3.7/site-packages/pandas/io/parsers.py", line 2059, in read
data = self._reader.read(nrows)
File "pandas/_libs/parsers.pyx", line 881, in pandas._libs.parsers.TextReader.read
File "pandas/_libs/parsers.pyx", line 908, in pandas._libs.parsers.TextReader._read_low_memory
File "pandas/_libs/parsers.pyx", line 973, in pandas._libs.parsers.TextReader._read_rows
File "pandas/_libs/parsers.pyx", line 1105, in pandas._libs.parsers.TextReader._convert_column_data
File "pandas/_libs/parsers.pyx", line 1136, in pandas._libs.parsers.TextReader._convert_tokens
File "pandas/_libs/parsers.pyx", line 1232, in pandas._libs.parsers.TextReader._convert_with_dtype
ValueError: Integer column has NA values in column 3
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/Users/lorencm/projects/bioinf-scripts/reduceIsoforms.py", line 24, in <module>
df = read_gtf("data/hybrid.gtf")
File "/anaconda/envs/bioinf-scripts/lib/python3.7/site-packages/gtfparse/read_gtf.py", line 211, in read_gtf
restrict_attribute_columns=usecols)
File "/anaconda/envs/bioinf-scripts/lib/python3.7/site-packages/gtfparse/read_gtf.py", line 154, in parse_gtf_and_expand_attributes
features=features)
File "/anaconda/envs/bioinf-scripts/lib/python3.7/site-packages/gtfparse/read_gtf.py", line 122, in parse_gtf
raise ParsingError(str(e))
gtfparse.parsing_error.ParsingError: Integer column has NA values in column 3
Hi, I used the following GTF file from Scallop:
However, the belowe code caused the following errors:
This is the code:
What did I miss?
Thank you in advance,
Michal