Open chemgeeklian opened 5 years ago
I encountered the same problem with python 3.7. However, later I realized that it was probably coded based on python 2. After switching to python 2.7, I was able to execute the original code without any problem.
I encountered the same problem with python 3.7. However, later I realized that it was probably coded based on python 2. After switching to python 2.7, I was able to execute the original code without any problem.
I do not think it is the right way since python2 will be deprecated in 2020.
I encountered the same problem with python 3.7. However, later I realized that it was probably coded based on python 2. After switching to python 2.7, I was able to execute the original code without any problem.
I do not think it is the right way since python2 will be deprecated in 2020.
That is true. I have also tried using your solution and I think I got the same output as in python 2 in the tutorial. Why do you think that there should be 245 positions in the MSA instead of 205?
I encountered the same problem with python 3.7. However, later I realized that it was probably coded based on python 2. After switching to python 2.7, I was able to execute the original code without any problem.
I do not think it is the right way since python2 will be deprecated in 2020.
That is true. I have also tried using your solution and I think I got the same output as in python 2 in the tutorial. Why do you think that there should be 245 positions in the MSA instead of 205?
It's just my misunderstanding. Sorry for that.
I am having the same problem now. vapour@osman:~/pySCA-master$ /usr/local/miniconda2/bin/python2.7 ./scaProcessMSA.py Inputs/s1Ahalabi_1470_nosnakes.an -s 3TGI -c E -t -n >> Outputs/s1A_halabi.log /usr/local/miniconda2/lib/python2.7/site-packages/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 2569. PDBConstructionWarning) /usr/local/miniconda2/lib/python2.7/site-packages/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain I is discontinuous at line 2570. PDBConstructionWarning) /usr/local/miniconda2/lib/python2.7/site-packages/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain E is discontinuous at line 2580. PDBConstructionWarning) /usr/local/miniconda2/lib/python2.7/site-packages/Bio/PDB/StructureBuilder.py:91: PDBConstructionWarning: WARNING: Chain I is discontinuous at line 2758. PDBConstructionWarning) Error!!! Something wrong with PDBid or path...
I guess python 2 api is not supported anymore -- and things needs an update. if there is any solution outthere, ill be glad to hear it.
Cheers,
I found an issue related to the MSAsearch function in scaTools.py. I am new to python and just came up with a naive solution. But the output it not consist with that described in the pySCA tutorial.
Firstly I have ggsearch36 installed, which means I can use ggsearch36 in command lines :
And in python3, I tried ./scaProcessMSA.py Inputs/s1Ahalabi_1470_nosnakes.an -s 3TGI -c E -t -n to do MSA for the S1A family.
It gives error outputs:
After debugging for days I found this issue comes from this line in scaTools.py:
i_0 = [i for i in range(len(hd)) if output.split('\t')[1] in hd[i]]
It is that the byte type is not consist with str. I just solved it by modifying it to:
i_0 = [i for i in range(len(hd)) if output.split(b'\t')[1] in bytes(hd[i],'utf-8')]
It works and could give the final MSA outputs, but with 205 positions for S1A instead of 245.
Thank you very much for your help.