dinopy

• 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()