Comments (4)
Thank you, I fixed it.
Can you check it and close the issue if it works fine?
Thanks,
Arda
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Thanks! I just tried the new version, the initial error is gone, but I'm getting a new error now:
Traceback (most recent call last):
File "/home/jana/miniconda3/bin/gaftools", line 33, in <module>
sys.exit(load_entry_point('gaftools', 'console_scripts', 'gaftools')())
File "/home/jana/Downloads/test-gaftools/gaftools/gaftools/__main__.py", line 88, in main
module.main(args)
File "/home/jana/Downloads/test-gaftools/gaftools/gaftools/cli/stat.py", line 118, in main
run_stat(**vars(args))
File "/home/jana/Downloads/test-gaftools/gaftools/gaftools/cli/stat.py", line 50, in run_stat
for alignment_count, mapping in enumerate(parse_gaf(gaf_path), 1):
File "/home/jana/Downloads/test-gaftools/gaftools/gaftools/gaf.py", line 52, in parse_gaf
for line in open(filename):
File "/home/jana/miniconda3/lib/python3.7/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8b in position 1: invalid start byte
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Sounds like an encoding issue. @eblerjana, do you have a small example file? @asylvz Would be nice to turn this into a test case.
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It was a bug in parsing the GAF apparent in all the .gz files. Now it should be fine, I fixed it.
@tobiasmarschall, yes I agree.
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