A simple Python app to detect which of the DNA sequences in a test file are pieces of a given reference sequence. Reverse-complemented test sequences will also be matched.
To use, you will need a version of Python 3 installed (which you can access at https://www.python.org/downloads/).
To run, run the following in your CLI:
python -c "import SequenceMatcher; SequenceMatcher.findMatches(\"ref.fasta\",\"test.fasta\")"
ref.fasta and test.fasta can be replaced with paths for any reference sequence and test file respectively, as required. Included in this repo are an example ref.fasta containing the pol gene of HIV-1 and a test.fasta file containing HIV-1 contaminated with TB.
Output will be in the form of:
- A matches.fasta file containing all the pieces of sequence in test.fasta that were found in ref.fasta
- A mismatches.fasta file containing all the pieces of sequence in test.fasta that were not found in ref.fasta
- A summary of how many pieces of the sequence in matches.fasta and mismatches.fasta printed to the CLI
To run the tests, run
python SequenceMatcherTests.py