Error in importance_hdf5_to_bigwig.py requiring region_used argument
tli71193 opened this issue · 17 comments
Hi there
Ran into an error when running the contrib function where in importance_hdf5_to_bigwig.py
Traceback (most recent call last):
File "/net/gs/vol1/home/tli824/bin/software/chrombpnet/chrombpnet/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py", line 43, in <module>
main(args)
File "/net/gs/vol1/home/tli824/bin/software/chrombpnet/chrombpnet/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py", line 30, in main
regions = bigwig_helper.get_regions(args.regions, SEQLEN)
TypeError: get_regions() missing 1 required positional argument: 'regions_used'
I created a temporary work around/patch in the meantime by editing the get_regions function where regions_used = None by default
def get_regions(regions_file, seqlen, regions_used = None):
# regions file is assumed to be centered at summit (2nd + 10th column)
# it is adjusted to be of length seqlen centered at summit
assert(seqlen%2==0)
with open(regions_file) as r:
regions = [x.strip().split('\t') for x in r]
if regions_used:
regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions)[regions_used]]
else:
regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions)]
return regions
I have this same error
Hello,
Thank you for this, I will fix it today and keep you all posted.
Hello all,
Fixed this and made a new release. Feel free to reply back here or open another issue if you continue to see any errors or have questions.
Thank you,
Anu
Hi @panushri25 ,
I think this fix may have caused a new error when running chrombpnet contribs_bw since nothing is getting passed as regions_used.
Traceback (most recent call last):
File "/opt/conda/bin/chrombpnet", line 33, in <module>
sys.exit(load_entry_point('chrombpnet', 'console_scripts', 'chrombpnet')())
File "/scratch/chrombpnet/chrombpnet/CHROMBPNET.py", line 68, in main
importance_hdf5_to_bigwig.main(args_copy)
File "/scratch/chrombpnet/chrombpnet/evaluation/make_bigwigs/importance_hdf5_to_bigwig.py", line 30, in main
regions = bigwig_helper.get_regions(args.regions, SEQLEN)
File "/scratch/chrombpnet/chrombpnet/evaluation/make_bigwigs/bigwig_helper.py", line 41, in get_regions
regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions.values)[regions_used]]
File "/scratch/chrombpnet/chrombpnet/evaluation/make_bigwigs/bigwig_helper.py", line 41, in <listcomp>
regions = [[x[0], int(x[1])+int(x[9])-seqlen//2, int(x[1])+int(x[9])+seqlen//2, int(x[1])+int(x[9])] for x in np.array(regions.values)[regions_used]]
TypeError: only size-1 arrays can be converted to Python scalars
Best,
Robin
thank you for this, let me take a look. I did it test it even with empty regions_used, maybe its version specific.
Can you tell me your numpy version?
Numpy version is 1.23.4
Rest of my package versions if it's helpful:
absl-py 2.0.0
asttokens 2.4.1
astunparse 1.6.3
blosc2 2.3.1
boltons 23.0.0
brotlipy 0.7.0
cachetools 5.3.2
cairocffi 1.6.1
CairoSVG 2.7.1
certifi 2023.7.22
cffi 1.15.0
charset-normalizer 2.0.4
chrombpnet 0.1.5 /scratch/chrombpnet
cloudpickle 3.0.0
colorama 0.4.4
conda 23.7.4
conda-content-trust 0+unknown
conda-package-handling 1.8.1
contourpy 1.2.0
cryptography 36.0.0
cssselect2 0.7.0
cycler 0.12.1
decorator 5.1.1
deepdish 0.3.7
deeplift 0.6.13.0
defusedxml 0.7.1
dm-tree 0.1.8
exceptiongroup 1.1.3
executing 2.0.1
flatbuffers 23.5.26
fonttools 4.44.0
gast 0.5.4
google-auth 2.23.4
google-auth-oauthlib 0.4.6
google-pasta 0.2.0
grpcio 1.59.2
h5py 3.10.0
hdf5plugin 4.3.0
html5lib 1.1
idna 3.3
igraph 0.9.11
imageio 2.32.0
importlib-metadata 6.8.0
importlib-resources 6.1.1
ipython 8.17.2
jedi 0.19.1
joblib 1.3.2
jsonpatch 1.33
jsonpointer 2.4
keras 2.8.0
Keras-Preprocessing 1.1.2
kiwisolver 1.4.5
kundajelab-shap 1
lazy_loader 0.3
leidenalg 0.8.10
libclang 16.0.6
llvmlite 0.41.1
logomaker 0.8
Markdown 3.5.1
MarkupSafe 2.1.3
matplotlib 3.8.1
matplotlib-inline 0.1.6
matplotlib-venn 0.11.6
modisco 0.5.16.0
modisco-lite 2.0.7
msgpack 1.0.7
ndindex 1.7
networkx 3.2.1
numba 0.58.1
numexpr 2.8.7
numpy 1.23.4
oauthlib 3.2.2
opt-einsum 3.3.0
packaging 23.2
pandas 2.1.3
parso 0.8.3
pexpect 4.8.0
Pillow 10.0.1
pip 23.3.1
pluggy 1.3.0
prompt-toolkit 3.0.40
protobuf 3.20.0
psutil 5.9.6
ptyprocess 0.7.0
pure-eval 0.2.2
py-cpuinfo 9.0.0
pyasn1 0.5.0
pyasn1-modules 0.3.0
pyBigWig 0.3.18
pycosat 0.6.3
pycparser 2.21
pyfaidx 0.6.1
Pygments 2.16.1
pyOpenSSL 22.0.0
pyparsing 3.1.1
pyphen 0.14.0
PySocks 1.7.1
python-dateutil 2.8.2
pytz 2023.3.post1
requests 2.27.1
requests-oauthlib 1.3.1
rsa 4.9
ruamel.yaml 0.17.10
ruamel.yaml.clib 0.2.2
ruamel-yaml-conda 0.15.100
scikit-image 0.22.0
scikit-learn 1.3.2
scipy 1.11.3
setuptools 61.2.0
six 1.16.0
stack-data 0.6.3
tables 3.9.1
tensorboard 2.8.0
tensorboard-data-server 0.6.1
tensorboard-plugin-wit 1.8.1
tensorflow 2.8.0
tensorflow-estimator 2.8.0
tensorflow-io-gcs-filesystem 0.34.0
tensorflow-probability 0.15.0
termcolor 2.3.0
texttable 1.7.0
tf-estimator-nightly 2.8.0.dev2021122109
threadpoolctl 3.2.0
tifffile 2023.9.26
tinycss2 1.2.1
toolz 0.12.0
tqdm 4.48.2
traitlets 5.13.0
typing_extensions 4.8.0
tzdata 2023.3
urllib3 1.26.8
wcwidth 0.2.9
WeasyPrint 52.5
webencodings 0.5.1
Werkzeug 3.0.1
wheel 0.37.1
wrapt 1.16.0
zipp 3.17.0
I believe the issue is that np.array()[None] adds a new axis. Using code similar to @tli71193 solved this for me.
@robinmeyers and @tli71193 Please update to the latest 0.1.6 version and regenerate your contribution scores. It should fix this error.
@tli71193 Your fix was helpful but it does not fully integrate the added functionality. So please try 0.1.6 and let me know if everything works okay.
@panushri25 Thanks for this fix! The latest version fixed contribs_bw for me, but now pred_bw is broken. I get this error:
Traceback (most recent call last):
File "/opt/conda/bin/chrombpnet", line 33, in <module>
sys.exit(load_entry_point('chrombpnet', 'console_scripts', 'chrombpnet')())
File "/scratch/chrombpnet/chrombpnet/CHROMBPNET.py", line 56, in main
predict_to_bigwig.main(args)
File "/scratch/chrombpnet/chrombpnet/evaluation/make_bigwigs/predict_to_bigwig.py", line 139, in main
regions = bigwig_helper.get_regions(args.regions, outputlen, regions_used) # output regions
File "/scratch/chrombpnet/chrombpnet/evaluation/make_bigwigs/bigwig_helper.py", line 41, in get_regions
if regions_used:
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
makes sense, fixing this
try 0.1.7 both should be working now
where is 0.1.7?
Thanks,
Yichao
Have you been installing using pip or from github?
Thanks for the quick reply! In the GitHub Release, there is no "0.1.7".
Yes. I do find it in pip. https://pypi.org/project/chrombpnet/
Thanks,
Yichao
yes, i will make it the latest on github once i close this issue
0.1.7 fixed the issue for me. Thanks!
Awesome thank for the update!