read_fasta is a one-stop-shop for reading in FASTA files! Customizable keywords allow a variety of sanitizing functions which include:
- Ignore, remove, or convert sequences with invalid amino acid characters (
B/U/X/*/-)- Ignore or remove duplicate sequences or duplicate FASTA records
- Alternatively, allow duplicate sequences, headers, and FASTA records (something most other parsers do not)
- Arbitrary conversion of amino acids via a customizable
correction_dictionary
Once parsed, read_fasta returns either a dictionary of header-to-sequence values or a nested list, where each sub-list contains two elements (header, sequence).
For usage examples see the example_label page. Full documentation is shown below.
protfasta
read_fasta