hlancpred 1.0
A tool for predicting and scanning the peptides with the ability to bind non-classical class-I HLA alleles
Requires Python: >=3.6

# HLAncPred
# Introduction
HLAncPred is developed for predicting and scanning the peptides with the ability to bind non-classical class-I HLA alleles such as HLA-G\*01:01,HLA-G\*01:03,HLA-G\*01:04, HLA-E\*01:01, HLA-E\*01:03 . More information on HLAncPred is available from its web-server https://webs.iiitd.edu.in/raghava/hlancpred/stand.html. This page provides information about stnadalone version of HLAncPred. Please read/cite the content about the HLAncPred for complete information including algorithm behind HLAncPred.

**Models:** In this program, five best models devoted to each allele, have been implemented for predicting the non-classical class-I HLA binder peptides. The models were trained on experimentally verified binders and randomly generated non-binders using Swiss-Prot database. 

**Modules/Jobs:** This program implements two modules (job types); i) Predict: for prediction of non-classical class-I HLA allele binder peptides, ii) Scan: for creating all possible overlapping peptides of given length (window) and computing binding  potential (score) of the overlapping peptides.

**Minimum USAGE:** Minimum usage is "python3 hlancpred.py -i peptide.fa -a G0101," where peptide.fa is a input fasta file, and 'G0101' is the name for HLA-G\*01:01 against which the binders will be predicted. This will predict the binding ability of sequence in fasta format against HLA-G\*01:01. It will use other parameters by default. It will save output in "outfile.csv" in CSV (comma seperated variables).

**Full Usage:** Following is complete list of all options, you may get these options by "python hlancpred.py -h" 
```
usage: hlancpred [-h] -i INPUT -a {G0101,G0103,G0104,E0101,E0103} [-o OUTPUT] [-j {1,2}] [-w {8,9,10,11,12,13,14,15}] [-d {1,2}]

```

Please provide following arguments
```
optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input: protein or peptide sequence in FASTA format or single sequence per line in single letter code
  -a {G0101,G0103,G0104,E0101,E0103}, --allele {G0101,G0103,G0104,E0101,E0103}
                        Please provide the name of allele for the prediction of binder peptides
  -o OUTPUT, --output OUTPUT
                        Output: File for saving results by default outfile.csv
  -j {1,2}, --job {1,2}
                        Job Type: 1:predict, and 2:scan, by default 1
  -w {8,9,10,11,12,13,14,15}, --winleng {8,9,10,11,12,13,14,15}
                        Window Length: 8 to 35 (scan mode only), by default 9
  -d {1,2}, --display {1,2}
                        Display: 1:Only binders, 2: All peptides, by default 1
```

**Input File:** It allow users to provide input in two format; i) FASTA format (standard) and ii) Simple Format. In case of simple format, file should have one peptide sequence in a single line in single letter code (eg. peptide.seq). 
**Note:**
1: In case of predict and design module (job), the length of peptide should be upto 15 amino acids. If a sequence with length more than 15 will be provided, the program will take first 15 residues, and ignore the rest. In case of scan module, minimum length of protein/peptide sequence should be equal to window length (pattern), see peptide.fa.
2: Program will ignore peptides having length less than 8 residues (e.g., protein.fa).

**Output File:** Program will save the results in the CSV format, in case user do not provide output file name, it will be stored in "outfile.csv".

**Allele:** The program needs the name of the allele as shown in the usage, it could be G0101, G0103, G0104, E0101, and E0103.