diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000000000000000000000000000000000000..8eaa9973fa395635f48f2358b30e96ef52edd2a1 --- /dev/null +++ b/LICENSE @@ -0,0 +1,21 @@ +The MIT License (MIT) + +Copyright (c) 2023 Sara Schulte, Alexander Dilthey, Gunnar Klau + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. diff --git a/README.md b/README.md index 7571ddf3e0de5118dd25afc6f30c8e6937a0d9bd..7cff9cfc57ac5d10ce975ae66453f4587af89ac7 100644 --- a/README.md +++ b/README.md @@ -31,3 +31,36 @@ To execute HOGVAX, call the python script with the necessary arguments, see the ```shell python hogvax.py <arguments> ``` +The `--help` argument gives the following list of arguments. + +```angular2html + -h, --help show this help message and exit + --k K, -k K Maximal length of vaccine sequence + --populations POPULATIONS [POPULATIONS ...], -pop POPULATIONS [POPULATIONS ...] + Target population(s). Default "World" + --peptides PEPTIDES, -pep PEPTIDES + Preprocessed peptide file with every peptide in a new + line. + --allele-frequencies F_DATA, -af F_DATA + (Normalized) allele frequency file. + --ba-threshold BA_THRESHOLD, -t BA_THRESHOLD + Binding affinities are converted to binary data, where + everything >= BA_THRESHOLD is set to 1. + --binding-affinities BA_MATRIX, -ba BA_MATRIX + Binding affinity file for input peptides and alleles. + --required_epitopes REQUIRED_EPITOPES, -epi REQUIRED_EPITOPES + File of peptides you want to be present in vaccine + --min-hits MIN_HITS, -mh MIN_HITS + Minimum number of hits for an allele to be covered + --maximize-peptides Maximize number of peptides in the vaccine in a second + optimization + --embedding-length EMBEDDING_LENGTH + Set length of embedding if used + --embedded-peptides EMBEDDED_PEPTIDES + File containing embedded peptides + --embedded-epitope_features EMBEDDED_EPITOPE_FEATURES + Path to embedded epitope features + --outdir OUTDIR, -o OUTDIR + Output directory + --verbose [LOGGING_ENABLED], -v [LOGGING_ENABLED] +``` \ No newline at end of file