This is a simple Python script for scanning sequences for epitopes.
python epitopescan.py <fasta file> <csv file> <output file>
<fasta file>
: in-frame nucleotide alignment<csv file>
: csv file with header:- the first column contains (linear) amino acid epitopes
- the second column contains a text description of the epitope
A tabulated file with the name of the sequence in the first column, and one column per epitope (0 for absent, 1 for present).
An example dataset is included of Ebola virus glycoprotein, along with a CSV file extracted from an Excel spreadsheet downloaded from the very useful LANL HFV database.
- Add option for regular expression searches
- Add option for position-specific (with respect to a reference sequence) epitopes
- Selene Zarate
- Simon Frost (@sdwfrost)
This code uses a collection of utilities in sequence.py
written by Selene Zarate; these have been modified slightly e.g. to accept different line termination characters.