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README.md

Fasta Filter

A simple program to remove sequences in a fasta file containing specific strings.

Usage

  1. Install python3.

  2. Run pip install -r ./requirements.txt if biopython is not installed. If installed, skip to step 2.

  3. Run ./fasta_filter.py -h if on Linux, or on Windows python3 ./fasta_filter -h. See help for more information.

Example Usage

  1. Pretend input.fasta exists in the same folder as fasta_filter.py (the program file).

  2. To remove all sequences in input.fasta that contain rt in the header and output to a new file called input_filtered.fasta, run: python3 ./fasta_filter.py input.fasta input_filtered.fasta -c rt