Thank you for putting together this package. I am trying to use it on some ATAC-seq data and having a few issues. Although your test data ran perfectly in the msCentipede I installed for some reason I can't run my own motif file and BAM files. The motif file is identically set up to yours and has the top 1000 motifs and PWM scores, its exported out of FIMO and edited to look exactly as yours does. Its attached. Error message:
loading motifs ...
num of motif sites = 0
loading read counts ...
Traceback (most recent call last):
File "call_binding.py", line 344, in
main()
File "call_binding.py", line 337, in main
learn_model(options)
File "call_binding.py", line 72, in learn_model
total_counts = np.sum(count_data, 2).T
File "//anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 1835, in sum
out=out, keepdims=keepdims)
File "//anaconda/lib/python2.7/site-packages/numpy/core/_methods.py", line 32, in _sum
return umr_sum(a, axis, dtype, out, keepdims)
ValueError: 'axis' entry is out of bounds
Please let me know what I may be doing wrong, thank you.
Hi Raj,
Thank you for putting together this package. I am trying to use it on some ATAC-seq data and having a few issues. Although your test data ran perfectly in the msCentipede I installed for some reason I can't run my own motif file and BAM files. The motif file is identically set up to yours and has the top 1000 motifs and PWM scores, its exported out of FIMO and edited to look exactly as yours does. Its attached. Error message:
loading motifs ... num of motif sites = 0 loading read counts ... Traceback (most recent call last): File "call_binding.py", line 344, in
main()
File "call_binding.py", line 337, in main
learn_model(options)
File "call_binding.py", line 72, in learn_model
total_counts = np.sum(count_data, 2).T
File "//anaconda/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 1835, in sum
out=out, keepdims=keepdims)
File "//anaconda/lib/python2.7/site-packages/numpy/core/_methods.py", line 32, in _sum
return umr_sum(a, axis, dtype, out, keepdims)
ValueError: 'axis' entry is out of bounds
Please let me know what I may be doing wrong, thank you.
Rob fimo1.txt.gz