NetChop/NetCTL/NetCTLpan Predictions tool - version 3.0
=============================================
Release Note
------------
2020-05-12
* This release will run only under Python 3.6 or higher.
Introduction:
-------------
The distributions 'IEDB_NetChop-3.0.tar.gz' contains methods for NetChop, NetCTL and NetCTLpan.
NetChop is a predictor of proteasomal processing based upon a neural network. NetCTL is a predictor
of T cell epitopes along a protein sequence. It also employs a neural network architecture. NetCTLpan
is an update to the original NetCTL server that allows for prediction of CTL epitope with restriction
to any MHC molecules of known protein sequence.
Prerequisites:
--------------
+ Python 3.6 or higher
* http://www.python.org/
+ TCSH
* http://www.tcsh.org/
- sudo apt-get install tcsh gawk
+ Python-pip and other python
* https://pypi.python.org/pypi/pip
- sudo apt-get install python-pip
+ Matplotlib
* http://matplotlib.org/
- Under Ubuntu: sudo apt-get install python-matplotlib
- Under RedHat: sudo pip install matplotlib>=1.5.3
Virtualenv:
--------------
Virtualenv is a tool to create isolated Python environments. Every environments has its own installation directories, that doesn’t share libraries with other virtualenv environments (and optionally doesn’t access the globally installed libraries either). You may use this to manage different python and libraries versions on your machine.
* https://virtualenv.pypa.io/
- sudo pip install virtualenv
Installation:
-------------
Unpack the tar.gz files (IEDB_NetChop-3.0.tar.gz)
$ tar -zxvf IEDB_NetChop-3.0.tar.gz
$ cd netchop
$ pip install -r requirements.txt
$ ./build.sh
Available prediction methods are:
---------------------------------
netchop, netctl, netctlpan
Available commands:
-------------------
python predict.py -m <method-name> input-file
python predict.py -m <method-name> [options] input-file
Options:
--version show program's version number and exit
-h, --help show this help message and exit
-m METHOD, --method=METHOD
Select a method from available method options.
-t THRESHOLD, --threshold=THRESHOLD
Threshold value(default: netchop=0.5).
-w TAP_WEIGHT, --tap_weight=TAP_WEIGHT
NetCTL/NetCTLpan specific: weight on TAP transport
efficiency (default=0.050000/0.025).
-c CLEAVAGE_WEIGHT, --cleavage_weight=CLEAVAGE_WEIGHT
NetCTL/NetCTLpan specific: weight on C terminal
cleavage (default: netctl=0.100000, netctlpan=0.225).
-p PRED_METHOD, --pred_method=PRED_METHOD
Prediction method for NetChop (default=0).
-s SUPERTYPE, --supertype=SUPERTYPE
NetCTL specific: supertype(default=A1).
-a ALLELE, --allele=ALLELE
NetCTLpan specific: allele(default=HLA-A02:01).
-l LENGTH, --length=LENGTH
NetCTLpan specific: length(default=9).
-e EPITOPE_THRESHOLD, --epitope_threshold=EPITOPE_THRESHOLD
NetCTLpan specific:
epitope_threshold(default=1.000000).
-n, --noplot Do not generate a plot.
-o PLOT_NAME, --outputplot=PLOT_NAME
The plot output path/name(default=plot).
Example:
--------
python predict.py -m netchop example/test.fsa
python predict.py --method=netchop example/test.fsa
Example regarding options:
--------
python predict.py --method netchop example/test.fsa
python predict.py --method netchop --threshold 0.7 example/test.fsa
python predict.py --method netchop --threshold 0.7 --pred_method 0 example/test.fsa
python predict.py --method netchop --threshold 0.7 --pred_method 1 example/test.fsa
python predict.py --method netchop --threshold 0.7 --pred_method 20S example/test.fsa
python predict.py -m netctl example/test.fsa
python predict.py -m netctl -c 0.15 example/test.fsa
python predict.py -m netctl -c 0.15 -w 0.05 example/test.fsa
python predict.py -m netctl -c 0.15 -w 0.05 -s B39 example/test.fsa
python predict.py -m netctl -c 0.15 -w 0.05 -s B39 -t 0.75 example/test.fsa
python predict.py --method netctlpan example/test.fsa
python predict.py --method netctlpan --allele HLA-A01:01 example/test.fsa
python predict.py --method netctlpan --allele HLA-A01:01 --length 8 example/test.fsa
python predict.py --method netctlpan --allele HLA-A01:01 --length 8 --threshold -99.9 example/test.fsa
python predict.py --method netctlpan --allele HLA-A01:01 --length 8 --threshold -99.9 --cleavage_weight 0.225 example/test.fsa
python predict.py --method netctlpan --allele HLA-A01:01 --length 8 --threshold -99.9 --cleavage_weight 0.225 --tap_weight 0.025 example/test.fsa
python predict.py --method netctlpan --allele HLA-A01:01 --length 8 --threshold -99.9 --cleavage_weight 0.225 --tap_weight 0.025 --epitope_threshold 1.0 example/test.fsa
Example to change plot output path/name:
--------
python predict.py --method netchop example/test.fsa --outputplot plot2
python predict.py -m netctl -o plot2 example/test.fsa
Example to output prediction text to file:
--------
python predict.py --method netchop example/test.fsa >prediction.txt
python predict.py --method netchop example/test.fsa >prediction.txt --outputplot plot2
python predict.py -m netctl -o plot2 example/test.fsa >prediction.txt
python predict.py -m netctl -o result/plot2 example/test.fsa >result/prediction.txt