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liukeweiaway / iMRM

Post-transcriptional modification site recognition
MIT License
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Error running test sequence with iMRM.py #2

Open isabela42 opened 1 week ago

isabela42 commented 1 week ago

I was getting this error when running the given example test from README:

python iMRM.py -i sequence.txt -o ccc.html -s Human -m all -t normal checking over Traceback (most recent call last): File "iMRM.py", line 33, in preproces.preprocesser(args.inputFile, args.outputFile, args.species, args.modification, args.threshold) File "/mnt/path/to/tools/iMRM/preproces.py", line 184, in preprocesser threshold) File "/mnt/path/to/tools/iMRM/predictType.py", line 30, in human_XG_iRNA_pse print(iMRMFeatureEtraction.nc(new_line, 21), iMRMFeatureEtraction.dnc(new_line, 21), iMRMFeatureEtraction.tnc(new_line, 21), iMRMFeatureEtraction.tenc(new_line, 21), iMRMFeatureEtraction.pnc(new_line, 21), iMRMFeatureEtraction.nd(new_line, 21), iMRMFeatureEtraction.dnd(new_line, 21), iMRMFeatureEtraction.ncp(new_line, 21), iMRMFeatureEtraction.dpcp(new_line, 21), iMRMFeatureEtraction.onehot(new_line, 21), *iMRMFeatureEtraction.dbe(new_line, 21), file=file_inter_pse) File "/mnt/path/to/tools/iMRM/featureEtraction/iMRMFeatureEtraction.py", line 36, in tnc tri_nucleotide_dict = {"".join(i): 0 for i in product(RNA, repeat=3)} NameError: name 'product' is not defined

My solution was to add from itertools import product to the start of /mnt/path/to/tools/iMRM/featureEtraction/iMRMFeatureEtraction.py. The program did not give any further errors after that and provided the ccc.html file as expected.

liukeweiaway commented 2 days ago

I was getting this error when running the given example test from README:

python iMRM.py -i sequence.txt -o ccc.html -s Human -m all -t normal checking over Traceback (most recent call last): File "iMRM.py", line 33, in preproces.preprocesser(args.inputFile, args.outputFile, args.species, args.modification, args.threshold) File "/mnt/path/to/tools/iMRM/preproces.py", line 184, in preprocesser threshold) File "/mnt/path/to/tools/iMRM/predictType.py", line 30, in human_XG_iRNA_pse print(iMRMFeatureEtraction.nc(new_line, 21), iMRMFeatureEtraction.dnc(new_line, 21), iMRMFeatureEtraction.tnc(new_line, 21), iMRMFeatureEtraction.tenc(new_line, 21), iMRMFeatureEtraction.pnc(new_line, 21), iMRMFeatureEtraction.nd(new_line, 21), iMRMFeatureEtraction.dnd(new_line, 21), iMRMFeatureEtraction.ncp(new_line, 21), iMRMFeatureEtraction.dpcp(new_line, 21), iMRMFeatureEtraction.onehot(new_line, 21), *iMRMFeatureEtraction.dbe(new_line, 21), file=file_inter_pse) File "/mnt/path/to/tools/iMRM/featureEtraction/iMRMFeatureEtraction.py", line 36, in tnc tri_nucleotide_dict = {"".join(i): 0 for i in product(RNA, repeat=3)} NameError: name 'product' is not defined

My solution was to add from itertools import product to the start of /mnt/path/to/tools/iMRM/featureEtraction/iMRMFeatureEtraction.py. The program did not give any further errors after that and provided the ccc.html file as expected.

Tell me the results of the pip list.

isabela42 commented 1 day ago

pip list /software/python/Python-3.6.1/lib/python3.6/site-packages/secretstorage/dhcrypto.py:16: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead from cryptography.utils import int_from_bytes /software/python/Python-3.6.1/lib/python3.6/site-packages/secretstorage/util.py:25: CryptographyDeprecationWarning: int_from_bytes is deprecated, use int.from_bytes instead from cryptography.utils import int_from_bytes Package Version Editable project location absl-py 0.15.0 adjustText 0.7.3 ago 0.0.9 alabaster 0.7.6 alembic 1.2.0 amqp 2.6.1 analysis 0.1.7 aniso8601 4.0.1 anndata 0.6.22.post1 annoy 1.13.0 appdirs 1.4.3 apptools 4.4.0 APScheduler 3.6.1 argcomplete 3.1.2 argh 0.27.2 asn1crypto 0.24.0 astor 0.6.2 astroid 2.1.0 astropy 3.2.1 astunparse 1.6.3 async-generator 1.10 atomicwrites 1.2.1 attrs 20.3.0 Automat 20.2.0 autopep8 1.2.1 aws-requests-auth 0.4.1 awscli 1.15.42 Babel 2.1.1 backcall 0.1.0 batchspawner 0.9.0.dev0 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