ibpa/deeppep

Deep proteome inference from peptide profiles

deeppep's Issues

Cleanup phase2

Code refactoring

Cleanup phase1

• Remove unnecessary files used during development
• Merge classes when necessary

Cannot convert ‘struct THDoubleTensor *’ to ‘struct THLongTensor *’

Hello,
I have configured my environment in Ubuntu by your description. However, when i run "python run.py ./data/18mix" or other test datasets, I encountered one error:

Have you ever had the same question? How can i make it run? thanks.

input sequence smaller than kernel size

Thank you for developed such a great tool to deal with protein inference!
Everything went smoothly when I used toy data, but once I feed my real data, DeepPep throw me an error:

/home/torch/install/bin/luajit: /home/torch/install/share/lua/5.1/nn/Container.lua:67:
In 1 module of nn.Sequential:
In 1 module of nn.Sequential:
/home/torch/install/share/lua/5.1/nn/THNN.lua:110: bad argument #2 to 'v' (input sequence smaller than kernel size. Got: 7, Expected: 8 at /home/torch/extra/nn/lib/THNN/generic/TemporalConvolution.c:34)
stack traceback:
[C]: in function 'v'
/home/torch/install/share/lua/5.1/nn/THNN.lua:110: in function 'TemporalConvolution_updateOutput'
...hare/lua/5.1/sparsenn/SparseBlockTemporalConvolution.lua:109: in function 'pri_updateOutput_column'
...hare/lua/5.1/sparsenn/SparseBlockTemporalConvolution.lua:124: in function <...hare/lua/5.1/sparsenn/SparseBlockTemporalConvolution.lua:117>
[C]: in function 'xpcall'
/home/torch/install/share/lua/5.1/nn/Container.lua:63: in function 'rethrowErrors'
...e/torch/install/share/lua/5.1/nn/Sequential.lua:44: in function <...e/torch/install/share/lua/5.1/nn/Sequential.lua:41>
[C]: in function 'xpcall'
/home/torch/install/share/lua/5.1/nn/Container.lua:63: in function 'rethrowErrors'
...e/torch/install/share/lua/5.1/nn/Sequential.lua:44: in function 'forward'
/mnt/d/MSTools/DeepPep/CExperiment.lua:33: in function 'roundTrip'
trainPred.lua:37: in main chunk
[C]: in function 'dofile'
...hang/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk
[C]: at 0x7fa77820ff50

WARNING: If you see a stack trace below, it doesn't point to the place where this error occurred. Please use only the one above.
stack traceback:
[C]: in function 'error'
/home/torch/install/share/lua/5.1/nn/Container.lua:67: in function 'rethrowErrors'
...e/torch/install/share/lua/5.1/nn/Sequential.lua:44: in function 'forward'
/mnt/d/MSTools/DeepPep/CExperiment.lua:33: in function 'roundTrip'
trainPred.lua:37: in main chunk
[C]: in function 'dofile'
...hang/torch/install/lib/luarocks/rocks/trepl/scm-1/bin/th:150: in main chunk
[C]: at 0x7fa77820ff50

Could you please help me check with it?
Thanks!