rotifer.genome.io.gff#

rotifer.genome.io.gff(path, seqid=None, organism=None, strain=None, description=None, topology='linear', keywords=[], ete3=None)[source]#

Parse GFF file

Arguments:

  • path : file path or file handle

  • seqidrename sequence identifiers using a user-defined function
    This function will be given two arguments:

    • the sequence object (a Bio.SeqRecord.SeqRecord object)

    • the input file path

  • descriptionset sequence description

    Could be a lambda function with two arguments: file path and Bio.SeqRecord

  • organism : organism name or NCBI taxid

  • strainadd this string to the organism name but not to its taxonomy

    Could be a lambda function with two arguments: file path and Bio.SeqRecord

  • topology : sequence topology, circular or linear

  • keywords : keywords to add to annotation

  • ete3 : ete3 object to use when fetching taxonomy