# 💻 bioino

Command-line tools and Python API for interconverting FASTA, GFF, and CSV.

bioino currently converts tables to FASTA, and GFF to tables. Also provides a Python API for handling GFF and FASTA files, and converting to table files.

Note

bioino is under active development, and not fully tested, so things may change, break, or simply not work.

• Installation
  • The easy way
  • From source
• Usage
  • Command line
    • Detailed usage
  • Python API
    • FASTA
    • GFF
    • GFF lookup table
    • Interconversion
• bioino
  • bioino package
    • Submodules
    • bioino.cli module
      • main()
    • bioino.fasta module
      • FastaCollection
        • FastaCollection.sequences
        • FastaCollection.from_file()
        • FastaCollection.write()
        • FastaCollection.ATCG()
        • FastaCollection.GGGAAAA()
        • FastaCollection.from_file()
        • FastaCollection.from_pandas()
        • FastaCollection.sequences
        • FastaCollection.write()
      • FastaSequence
        • FastaSequence.name
        • FastaSequence.description
        • FastaSequence.sequence
        • FastaSequence.__str__()
        • FastaSequence.description
        • FastaSequence.name
        • FastaSequence.sequence
        • FastaSequence.write()
    • bioino.gff module
      • GffColumns
        • GffColumns.seqid
        • GffColumns.source
        • GffColumns.feature
        • GffColumns.start
        • GffColumns.end
        • GffColumns.score
        • GffColumns.strand
        • GffColumns.phase
        • GffColumns.__str__()
        • GffColumns.as_dict()
        • GffColumns.end
        • GffColumns.feature
        • GffColumns.phase
        • GffColumns.score
        • GffColumns.seqid
        • GffColumns.source
        • GffColumns.start
        • GffColumns.strand
      • GffFile
        • GffFile.lines
        • GffFile.metadata
        • GffFile.lookup
        • GffFile.as_dict()
        • GffFile.from_file()
        • GffFile.write()
        • GffFile.as_dict()
        • GffFile.from_file()
        • GffFile.lines
        • GffFile.lookup
        • GffFile.metadata
        • GffFile.to_csv()
        • GffFile.write()
      • GffLine
        • GffLine.metadata
        • GffLine.columns
        • GffLine.attributes
        • GffLine.copy()
        • GffLine.__str__()
        • GffLine.as_dict()
        • GffLine.attributes
        • GffLine.columns
        • GffLine.copy()
        • GffLine.from_dict()
        • GffLine.write()
      • GffMetadata
        • GffMetadata.metadata
        • GffMetadata.__str__()
        • GffMetadata.write()
        • GffMetadata.data
        • GffMetadata.write()
      • GffMetadatum
        • GffMetadatum.name
        • GffMetadatum.flag
        • GffMetadatum.values
        • GffMetadatum.__str__()
        • GffMetadatum.write()
        • GffMetadatum.flag
        • GffMetadatum.name
        • GffMetadatum.values
        • GffMetadatum.write()
    • bioino.tables module
    • Module contents

Source

Find the source code and issue tracker at GitHub.