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I am using Python 3.6.15 in Ubuntu 20.04 (Running inside a Docker container). The packages that I use are listed in the attached text file packages_python.txt
I want to generate evidence/msms/peptide files from a Prosit spectral library that I have. However, when I run the following command:
I get the error NameError: name 'atom2mass' is not defined. The full error log:
Using TensorFlow backend.
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:521: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
Traceback (most recent call last):
File "postprocess/main.py", line 175, in
class Spectrum:
File "postprocess/main.py", line 219, in Spectrum
for aa, formula in aa2formula.items()}
File "postprocess/main.py", line 219, in
for aa, formula in aa2formula.items()}
File "postprocess/main.py", line 218, in
aa2mass = {aa: (sum([atom2mass[atom] * cnt for atom, cnt in formula.items()]) - 2 * atom2mass['H'] - atom2mass['O'])
NameError: name 'atom2mass' is not defined
Any idea what could be wrong here?
Best,
Marc
The text was updated successfully, but these errors were encountered:
We ended up solving the error by adding a pre-calculated aa2mass object to the script and commenting out the original list comprehension line used to calculate aa2mass.
Hi,
I am using Python 3.6.15 in Ubuntu 20.04 (Running inside a Docker container). The packages that I use are listed in the attached text file
packages_python.txt
I want to generate evidence/msms/peptide files from a Prosit spectral library that I have. However, when I run the following command:
python3.6 postprocess/main.py prosit postprocess/parameters.json
I get the error NameError: name 'atom2mass' is not defined. The full error log:
Using TensorFlow backend.
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:517: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint8 = np.dtype([("qint8", np.int8, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:518: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint16 = np.dtype([("qint16", np.int16, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:521: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
_np_qint32 = np.dtype([("qint32", np.int32, 1)])
/usr/local/lib/python3.6/dist-packages/tensorflow/python/framework/dtypes.py:526: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
np_resource = np.dtype([("resource", np.ubyte, 1)])
Traceback (most recent call last):
File "postprocess/main.py", line 175, in
class Spectrum:
File "postprocess/main.py", line 219, in Spectrum
for aa, formula in aa2formula.items()}
File "postprocess/main.py", line 219, in
for aa, formula in aa2formula.items()}
File "postprocess/main.py", line 218, in
aa2mass = {aa: (sum([atom2mass[atom] * cnt for atom, cnt in formula.items()]) - 2 * atom2mass['H'] - atom2mass['O'])
NameError: name 'atom2mass' is not defined
Any idea what could be wrong here?
Best,
Marc
The text was updated successfully, but these errors were encountered: