jhkorhonen / MOODS

MOODS: Motif Occurrence Detection Suite
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TypeError specifically when using --best-hits #46

Open plger opened 1 year ago

plger commented 1 year ago

Hi,

I can run the following correctly:

moods-dna.py -S pwm.adm -s test.fasta -p 0.001

However when I try to use the best hit per sequence using the same pwm/fasta, I get the following error:

moods-dna.py -S pwm.adm -s test.fasta -B 1
Traceback (most recent call last):
  File "/conda/bin/moods-dna.py", line 4, in <module>
    __import__('pkg_resources').run_script('MOODS-python==1.9.4.1', 'moods-dna.py')
  File "/conda/lib/python3.6/site-packages/pkg_resources/__init__.py", line 651, in run_script
    self.require(requires)[0].run_script(script_name, ns)
  File "/conda/lib/python3.6/site-packages/pkg_resources/__init__.py", line 1448, in run_script
    exec(code, namespace, namespace)
  File "/conda/lib/python3.6/site-packages/MOODS_python-1.9.4.1-py3.6-linux-x86_64.egg-info/scripts/moods-dna.py", line 322, in <module>
    results = MOODS.scan.scan_best_hits_dna(seq, matrices_all, N)
  File "/conda/lib/python3.6/site-packages/MOODS/scan.py", line 1328, in scan_best_hits_dna
    return _scan.scan_best_hits_dna(seq, matrices, target, iterations, MULT, LIMIT_MULT, window_size)
TypeError: Wrong number or type of arguments for overloaded function 'scan_best_hits_dna'.
  Possible C/C++ prototypes are:
    MOODS::scan::scan_best_hits_dna(std::string const &,std::vector< score_matrix,std::allocator< score_matrix > > const &,size_t,int,unsigned int,size_t,size_t)
    MOODS::scan::scan_best_hits_dna(std::string const &,std::vector< score_matrix,std::allocator< score_matrix > > const &,size_t,int,unsigned int,size_t)
    MOODS::scan::scan_best_hits_dna(std::string const &,std::vector< score_matrix,std::allocator< score_matrix > > const &,size_t,int,unsigned int)
    MOODS::scan::scan_best_hits_dna(std::string const &,std::vector< score_matrix,std::allocator< score_matrix > > const &,size_t,int)
    MOODS::scan::scan_best_hits_dna(std::string const &,std::vector< score_matrix,std::allocator< score_matrix > > const &,size_t)

I've tried both installing MOODS via bioconda (above), as well as downloading and compiling 1.9.4.1 from source, and both give the same error.

Running on Ubuntu 18.04 LTS (GNU/Linux 4.15.0-23-generic x86_64) with Python 3.6.10 & g++ 7.5.0

Any tip would be welcome!