fqfa

fqfa is a pure Python library for bioinformatics and computational biology. It implements parsers for FASTA and FASTQ files as well as some commonly-used sequence operations.

To cite fqfa please refer to “fqfa: A pure Python package for genomic sequence files”.

Install fqfa from PyPI using pip:

pip3 install fqfa

To install the package for development purposes, include the optional dependencies:

pip3 install fqfa[dev]

Building a local copy of the documentation requires the following additional packages:

pip3 install sphinx
pip3 install sphinx-rtd-theme

• Usage examples
  • Basic sequence validation
  • Translating FASTA sequences
  • Filtering paired-end FASTQ reads on sequence quality
• File handling
  • has_fasta_ext()
  • has_fastq_ext()
  • open_compressed()
  • FASTA files
  • FASTQ files
• Sequence validation
  • amino_acids_all_validator()
  • amino_acids_validator()
  • dna_bases_validator()
  • dna_characters_validator()
  • rna_bases_validator()
  • create_validator()
  • IUPAC codes
• Utility functions
  • Nucleotide sequence utility functions
  • Coding sequence translation
  • Sequence type inference functions
• Performance comparison
  • Benchmarking for raw FASTQ files
  • Benchmarking for gzip-compressed FASTQ files
  • Benchmarking for bzip2-compressed FASTQ files