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View Code? Open in Web Editor NEWGRAph-based Finding of Individual Motif Occurrences
License: MIT License
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GRAFIMO repeatedly extracting regions from graph for each motif
Hi,
I am trying to use GRAFIMO to scan multiple motifs in a genome graph.
I passed in a MEME file with roughly 300 motifs defined in it.
The tools works fine, but every time it finishes with one motif in the file and moves to the next one, it re-extracts all the regions defined in the BED file.
I am not sure it is necessary for the tool to do that, and maybe this time costly step could be avoided?
Here is an example of the output logs I am getting:
***************************************************************************
Welcome to GRAFIMO v1.1.4
***************************************************************************
Read 344 motifs in motifs.meme
Processing motifs
Progress: [==================================================] 100.0% Complete
Extracting regions defined in regions.bed.
Progress: [==================================================] 100.0% Complete
Scoring hits for motif +MA0816.1.
Scoring hits for motif -MA0816.1.
Progress: [==================================================] 100.0% Complete
Computing q-values...
Scanned sequences: 136064
Scanned nucleotides: 1360640
Writing results in epi_motifs.
Extracting regions defined in regions.bed.
Progress: [ ] 0.0% Complete
Progress: [==================================================] 100.0% Complete
Scoring hits for motif +MA1632.1.
Scoring hits for motif -MA1632.1.
Progress: [==================================================] 100.0% Complete
...
numba.errors.TypingError in findmotif tutorial
Hello, @kant and @ManuelTgn,
Thank you for creating GRAFIMO! I would like to use it, but I have encountered errors, that I failed to resolve. I have tried to go through the tutorial for finding motifs and got the following error
Traceback (most recent call last):
File "/usr/lib64/python3.6/multiprocessing/process.py", line 258, in _bootstrap
self.run()
File "/usr/lib64/python3.6/multiprocessing/process.py", line 93, in run
self._target(*self._args, **self._kwargs)
File "/home/lokorokova/.local/lib/python3.6/site-packages/grafimo/score_sequences.py", line 271, in score_seqs
seq, score_matrix, pval_mat, min_score, scale, width, offset
File "/usr/lib64/python3.6/site-packages/numba/dispatcher.py", line 330, in _compile_for_args
raise e
File "/usr/lib64/python3.6/site-packages/numba/dispatcher.py", line 307, in _compile_for_args
return self.compile(tuple(argtypes))
File "/usr/lib64/python3.6/site-packages/numba/dispatcher.py", line 579, in compile
cres = self._compiler.compile(args, return_type)
File "/usr/lib64/python3.6/site-packages/numba/dispatcher.py", line 80, in compile
flags=flags, locals=self.locals)
File "/usr/lib64/python3.6/site-packages/numba/compiler.py", line 779, in compile_extra
return pipeline.compile_extra(func)
File "/usr/lib64/python3.6/site-packages/numba/compiler.py", line 362, in compile_extra
return self._compile_bytecode()
File "/usr/lib64/python3.6/site-packages/numba/compiler.py", line 738, in _compile_bytecode
return self._compile_core()
File "/usr/lib64/python3.6/site-packages/numba/compiler.py", line 725, in _compile_core
res = pm.run(self.status)
File "/usr/lib64/python3.6/site-packages/numba/compiler.py", line 248, in run
raise patched_exception
File "/usr/lib64/python3.6/site-packages/numba/compiler.py", line 240, in run
stage()
File "/usr/lib64/python3.6/site-packages/numba/compiler.py", line 454, in stage_nopython_frontend
self.locals)
File "/usr/lib64/python3.6/site-packages/numba/compiler.py", line 881, in type_inference_stage
infer.propagate()
File "/usr/lib64/python3.6/site-packages/numba/typeinfer.py", line 846, in propagate
raise errors[0]
File "/usr/lib64/python3.6/site-packages/numba/typeinfer.py", line 137, in propagate
constraint(typeinfer)
File "/usr/lib64/python3.6/site-packages/numba/typeinfer.py", line 503, in __call__
self.resolve(typeinfer, typeinfer.typevars, fnty=self.func)
File "/usr/lib64/python3.6/site-packages/numba/typeinfer.py", line 452, in resolve
raise TypingError(msg, loc=self.loc)
numba.errors.TypingError: Failed at nopython (nopython frontend)
Invalid usage of getitem with parameters (str, int64)
* parameterized
File "../../home/lokorokova/.local/lib/python3.6/site-packages/grafimo/score_sequences.py", line 340
[1] During: typing of intrinsic-call at /home/lokorokova/.local/lib/python3.6/site-packages/grafimo/score_sequences.py (340)
The whole log is attached as a file.
grafimo.log
Versions of packages, used in this case
vg version v1.43.0
pandas 1.1.5
numpy 1.19.5
statsmodels 0.12.2
sphinx 5.1.1
numba 0.53.1
colorama 0.4.5
I would be very grateful for help!
Larsa
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