Invalid file path or buffer object type: <class 'deepcpg.data.utils.GzipFile'>
dnaase opened this issue · 10 comments
Hi,
Thanks for making this software. After I download the example data files (by script in deepcpg/examples/setup.sh), when I am running the example script:
python deepcpg_path/dcpg_data.py --cpg_profiles ../data/cpg/BS27_1_SER.tsv.gz ../data/cpg/BS27_3_SER.tsv.gz ../data/cpg/BS27_5_SER.tsv.gz ../data/cpg/BS27_6_SER.tsv.gz ../data/cpg/BS27_8_SER.tsv.gz --dna_files ../data/dna/mm10 --out_dir ./data --dna_wlen 1001 --cpg_wlen 50 --nb_sample 1000
I got the problem of this error. It seems something is wrong about reading the file, but i have checked that all of the files path are correct in my system...
Traceback (most recent call last):
File "/home/yaping/software/deepcpg/deepcpg/scripts/dcpg_data.py", line 629, in
app.run(sys.argv)
File "/home/yaping/software/deepcpg/deepcpg/scripts/dcpg_data.py", line 260, in run
return self.main(name, opts)
File "/home/yaping/software/deepcpg/deepcpg/scripts/dcpg_data.py", line 413, in main
log=log.info)
File "/home/yaping/software/deepcpg/deepcpg/scripts/dcpg_data.py", line 114, in read_cpg_profiles
cpg_profile = dat.read_cpg_profile(cpg_file, sort=True, *args, **kwargs)
File "build/bdist.linux-x86_64/egg/deepcpg/data/utils.py", line 254, in read_cpg_profile
File "/home/yaping/software/anaconda/anaconda2/envs/ccimpute/lib/python2.7/site-packages/pandas/io/parsers.py", line 655, in parser_f
return _read(filepath_or_buffer, kwds)
File "/home/yaping/software/anaconda/anaconda2/envs/ccimpute/lib/python2.7/site-packages/pandas/io/parsers.py", line 392, in _read
filepath_or_buffer, encoding, compression)
File "/home/yaping/software/anaconda/anaconda2/envs/ccimpute/lib/python2.7/site-packages/pandas/io/common.py", line 210, in get_filepath_or_buffer
raise ValueError(msg.format(_type=type(filepath_or_buffer)))
ValueError: Invalid file path or buffer object type: <class 'deepcpg.data.utils.GzipFile'>
@dnaase, can you send me the output of pip list? Pandas seems to cause the problem.
Package Version
backports-abc 0.5
backports.shutil-get-terminal-size 1.0.0
backports.ssl-match-hostname 3.4.0.2
cycler 0.10.0
decorator 4.0.11
deepcpg 1.0.4
enum34 1.1.6
funcsigs 1.0.2
functools32 3.2.3.post2
h5py 2.7.0
ipykernel 4.6.1
ipython 5.3.0
ipython-genutils 0.2.0
jupyter-client 5.0.1
jupyter-core 4.3.0
Keras 1.2.2
matplotlib 2.0.2
mock 2.0.0
multitables 1.1.0
mxnet 0.9.4
numexpr 2.6.2
numpy 1.12.1
pandas 0.20.1
pathlib2 2.2.1
pbr 3.0.1
pexpect 4.2.1
pickleshare 0.7.4
pip 9.0.1
prompt-toolkit 1.0.14
protobuf 3.3.0
ptyprocess 0.5.1
py 1.4.33
Pygments 2.2.0
pyparsing 2.2.0
pytest 3.0.7
python-dateutil 2.6.0
pytz 2017.2
PyYAML 3.12
pyzmq 16.0.2
scandir 1.5
scikit-learn 0.18.1
scipy 0.19.0
seaborn 0.7.1
setuptools 27.2.0
simplegeneric 0.8.1
singledispatch 3.4.0.3
six 1.10.0
sklearn 0.0
subprocess32 3.2.7
tables 3.4.2
tensorflow 1.1.0
tensorflow-gpu 1.1.0
tftables 1.1.1
Theano 0.9.0
tornado 4.5.1
traitlets 4.3.2
wcwidth 0.1.7
Werkzeug 0.12.2
wheel 0.29.0
pandas 0.20.1 caused the problem. Checkout the latest master version, then it should work.
pandas 0.20.1 is the newest released version. Do you mean I should re-compile and use the newest github master version of pandas?
I also tried the older version of pandas, it does not work..
Please run pip install -U pandas and git pull in your DeepCpG directory. Then try it again and send me the error message if it still does not work.
Thanks for the package. I'm getting a similar error using pandas 0.20.3
Traceback (most recent call last):
File "/home/hasan/anaconda3/bin/dcpg_data.py", line 630, in
app.run(sys.argv)
File "/home/hasan/anaconda3/bin/dcpg_data.py", line 261, in run
return self.main(name, opts)
File "/home/hasan/anaconda3/bin/dcpg_data.py", line 414, in main
log=log.info)
File "/home/hasan/anaconda3/bin/dcpg_data.py", line 115, in read_cpg_profiles
cpg_profile = dat.read_cpg_profile(cpg_file, sort=True, *args, **kwargs)
File "/home/hasan/anaconda3/lib/python3.6/site-packages/deepcpg/data/utils.py", line 182, in read_cpg_profile
usecols=usecols, dtype=dtype, skiprows=skiprows)
File "/home/hasan/anaconda3/lib/python3.6/site-packages/pandas/io/parsers.py", line 655, in parser_f
return _read(filepath_or_buffer, kwds)
File "/home/hasan/anaconda3/lib/python3.6/site-packages/pandas/io/parsers.py", line 392, in _read
filepath_or_buffer, encoding, compression)
File "/home/hasan/anaconda3/lib/python3.6/site-packages/pandas/io/common.py", line 210, in get_filepath_or_buffer
raise ValueError(msg.format(_type=type(filepath_or_buffer)))
ValueError: Invalid file path or buffer object type: <class 'deepcpg.data.utils.GzipFile'>
Installing pandas 0.19.2 should fix this issue:
pip install pandas==0.19.2
pandas 0.19.2 indeed fix it