dinopy package

• dinopy.auxiliary module
  • qgram_generator()
• dinopy.conversion module
  • basenumbers_to_bytes()
  • basenumbers_to_string()
  • bytes_to_basenumbers()
  • bytes_to_string()
  • decode()
  • decode_fourbit()
  • decode_twobit()
  • encode()
  • encode_fourbit()
  • encode_twobit()
  • get_inverse_codemap_from_twobit()
  • illumina13_to_phred()
  • illumina15_to_phred()
  • illumina18_to_phred()
  • phred_to_illumina13()
  • phred_to_illumina15()
  • phred_to_illumina18()
  • phred_to_sanger()
  • phred_to_solexa()
  • sanger_to_phred()
  • solexa_to_phred()
  • string_list_to_basenumbers()
  • string_sublists_to_basenumbers()
  • string_to_basenumbers()
  • string_to_bytes()
• dinopy.creader module
  • CReader
    • CReader.close()
    • CReader.closed
    • CReader.fileno()
    • CReader.flush()
    • CReader.isatty()
    • CReader.open()
    • CReader.read()
    • CReader.readable()
    • CReader.readinto()
    • CReader.readline()
    • CReader.readlines()
    • CReader.seek()
    • CReader.seekable()
    • CReader.tell()
    • CReader.truncate()
    • CReader.writable()
    • CReader.writelines()
• dinopy.definitions module
  • FastaChromosomeC
    • FastaChromosomeC.__getitem__()
    • FastaChromosomeC.length
    • FastaChromosomeC.name
    • FastaChromosomeC.sequence
  • FastaChromosomeInfoC
    • FastaChromosomeInfoC.__getitem__()
    • FastaChromosomeInfoC.interval
    • FastaChromosomeInfoC.length
    • FastaChromosomeInfoC.name
  • FastaEntryC
    • FastaEntryC.__getitem__()
    • FastaEntryC.interval
    • FastaEntryC.length
    • FastaEntryC.name
    • FastaEntryC.sequence
  • FastaGenomeC
    • FastaGenomeC.__getitem__()
    • FastaGenomeC.info
    • FastaGenomeC.sequence
  • FastaReadC
    • FastaReadC.__getitem__()
    • FastaReadC.name
    • FastaReadC.sequence
  • FastqLineC
    • FastqLineC.__getitem__()
    • FastqLineC.type
    • FastqLineC.value
  • FastqReadC
    • FastqReadC.__getitem__()
    • FastqReadC.name
    • FastqReadC.quality
    • FastqReadC.sequence
  • FastqReadWithoutNameC
    • FastqReadWithoutNameC.__getitem__()
    • FastqReadWithoutNameC.quality
    • FastqReadWithoutNameC.sequence
  • FastqReadWithoutQVC
    • FastqReadWithoutQVC.__getitem__()
    • FastqReadWithoutQVC.name
    • FastqReadWithoutQVC.sequence
  • IUPACRandomReplacementDict
    • IUPACRandomReplacementDict.__getitem__()
  • basenumbers
  • bit_base
  • four_bit
  • two_bit
• dinopy.exceptions
  • ChromosomeFormatError
  • InvalidDtypeError
  • InvalidEncodingError
  • InvalidIUPACAmbiguityCodeError
  • InvalidLinetypeError
  • InvalidStartingCharacterError
  • MalformedFASTAError
  • TooManyCharactersError
  • UnknownCharactersError
• dinopy.fai_io module
  • chromosome_info_to_fai()
  • fai_entry_to_chromosome_info_entry()
  • fai_to_chromosome_info()
  • is_valid_fai()
  • is_valid_fai_entry()
  • read_fai()
  • write_chromosomes_as_fai()
  • write_fai()
• dinopy.fasta_writer module
  • FastaWriter
    • FastaWriter.close()
    • FastaWriter.write_chromosome()
    • FastaWriter.write_chromosomes()
    • FastaWriter.write_entries()
    • FastaWriter.write_entry()
    • FastaWriter.write_genome()
• dinopy.fasta_reader module
  • FastaReader
    • FastaReader.chromosomes()
    • FastaReader.entries()
    • FastaReader.genome()
    • FastaReader.lines()
    • FastaReader.random_access()
    • FastaReader.reads()
• dinopy.fastq_writer module
  • FastqWriter
    • FastqWriter.write()
    • FastqWriter.write_reads()
• dinopy.fastq_reader module
  • FastqReader
    • FastqReader.guess_quality_format()
    • FastqReader.lines()
    • FastqReader.print_quality_tally()
    • FastqReader.quality_tally
    • FastqReader.reads()
• dinopy.input_opener module
  • InputOpener
• dinopy.nameline_parser module
  • NamelineParser
    • NamelineParser.parse()
  • parse_casava_18_line()
  • parse_casava_pre18_line()
  • parse_ncbi_line()
• dinopy.processors module
  • complement()
  • complement_2bit()
  • complement_4bit()
  • qgrams()
  • replace_ambiguities()
  • reverse_complement()
  • reverse_complement_2bit()
  • reverse_complement_4bit()
  • suffix_array()
• dinopy.sambam module
  • AlignmentRecord
    • AlignmentRecord.cigar
    • AlignmentRecord.flag
    • AlignmentRecord.fromdict()
    • AlignmentRecord.fromkeywords()
    • AlignmentRecord.fromstr()
    • AlignmentRecord.fromvalues()
    • AlignmentRecord.get_sam_repr()
    • AlignmentRecord.mapping_quality
    • AlignmentRecord.optional
    • AlignmentRecord.optional_raw
    • AlignmentRecord.pnext
    • AlignmentRecord.pos
    • AlignmentRecord.qual
    • AlignmentRecord.query_name
    • AlignmentRecord.query_sequence
    • AlignmentRecord.rname
    • AlignmentRecord.rnext
    • AlignmentRecord.template_length
  • cigar_str_from_pysam_cigartuples()
  • cigar_str_from_tuples()
  • create_flag()
  • get_flag_description()
  • pysam_cigartuples_from_cigar_str()
  • tuples_from_cigar_str()
• dinopy.sam_reader module
  • SamReader
    • SamReader.get_header()
    • SamReader.records()
• dinopy.sam_writer module
  • SamWriter
    • SamWriter.close()
    • SamWriter.create_header_sq_lines()
    • SamWriter.write_header()
    • SamWriter.write_header_line()
    • SamWriter.write_record()
    • SamWriter.write_records()
    • SamWriter.write_sq_header()
• dinopy.shape module
  • Shape
    • Shape.bool_shape
    • Shape.index_shape_care
    • Shape.index_shape_dont_care
    • Shape.length
    • Shape.num_care
    • Shape.num_dont_care
    • Shape.is_solid()
• dinopy.shaping module
  • apply_shape()
  • windows()
  • windows_list()