Find the version of installed NetMHCIIpan automatically
Current Behavior:
...../PANDORA/PANDORA/Pandora/Modelling_functions.py in predict_anchors_netMHCIIpan(peptide, allele_type, verbose)
--> 123 with open(PANDORA.PANDORA_path + '/../netMHCIIpan-4.0/data/allele.list') as f:
124 for line in f:
125 all_netMHCpan_alleles.append(line.replace('\n', ''))
FileNotFoundError: [Errno 2] No such file or directory: '../PANDORA/../netMHCIIpan-4.0/data/allele.list'
Detailed Description:
The NetMHCIIpan fails because the version of the installed NetMHCIIpan is different from the one hardcoded in the /PANDORA/Pandora/Modelling_functions.py module.
Better to automatically extract the version.
The simplest way is to use the exact code in/PANDORA/PMHC/PMHC.py.
But the ideal way is to design to put the anchor prediction scripts in a different class (e.g. Anchors). So to reduce redundancy in code (e.g. copying the code to extract the installed version of NetMHcpan/NetMHCIIpan in different scripts)
DarioMarzella
commented
2 years ago
Find the version of installed NetMHCIIpan automatically
The NetMHCIIpan fails because the version of the installed NetMHCIIpan is different from the one hardcoded in the
/PANDORA/Pandora/Modelling_functions.pymodule. Better to automatically extract the version. The simplest way is to use the exact code in/PANDORA/PMHC/PMHC.py. But the ideal way is to design to put the anchor prediction scripts in a different class (e.g. Anchors). So to reduce redundancy in code (e.g. copying the code to extract the installed version of NetMHcpan/NetMHCIIpan in different scripts)