bx.seq package

Submodules

• bx.seq.core module
  • infer_format()
  • reverse_complement()
  • seq_file()
  • seq_reader()
  • seq_writer()
• bx.seq.fasta module
  • FastaFile
  • FastaReader
  • FastaWriter
    • FastaWriter.close()
    • FastaWriter.write()
• bx.seq.fasta_tests module
  • FASTATestCase
    • FASTATestCase.test_get()
  • check_get()
• bx.seq.nib module
  • nib file format
  • NibFile
    • NibFile.raw_fetch()
  • NibReader
  • NibWriter
    • NibWriter.close()
    • NibWriter.write()
• bx.seq.nib_tests module
  • NIBTestCase
    • NIBTestCase.test_get()
  • check_get()
• bx.seq.qdna module
  • qdna file format
  • QdnaCodebook
    • QdnaCodebook.read_codebook()
    • QdnaCodebook.vector_text()
  • QdnaFile
    • QdnaFile.get_quantum()
    • QdnaFile.raw_fetch()
    • QdnaFile.read_string()
    • QdnaFile.set_property()
  • QdnaReader
  • QdnaWriter
    • QdnaWriter.close()
    • QdnaWriter.write()
• bx.seq.qdna_tests module
  • QDNATestCase
    • QDNATestCase.test_get()
  • check_get()
• bx.seq.seq module
  • SeqFile
    • SeqFile.close()
    • SeqFile.extract_name()
    • SeqFile.get()
    • SeqFile.raw_fetch()
    • SeqFile.reverse_complement()
    • SeqFile.set_text()
  • SeqReader
    • SeqReader.close()
  • SeqReaderIter
• bx.seq.seq_tests module
  • SEQTestCase
    • SEQTestCase.test_get_fasta()
    • SEQTestCase.test_get_nib()
    • SEQTestCase.test_get_qdna()
    • SEQTestCase.test_get_reader()
  • check_get()
• bx.seq.twobit module
  • TwoBitFile
    • TwoBitFile.load_sequence()
    • TwoBitFile.read()
    • TwoBitFile.read_block_coords()
    • TwoBitFile.read_p_string()
  • TwoBitSequence
    • TwoBitSequence.get()
    • TwoBitSequence.masked_block_sizes
    • TwoBitSequence.masked_block_starts
    • TwoBitSequence.n_block_sizes
    • TwoBitSequence.n_block_starts
• bx.seq.twobit_tests module

Module contents

Classes for dealing with biological sequences. See core for the abstract sequence classes and nib and qdna for specifics of various formats.

bx.seq.infer_format(file)

bx.seq.reverse_complement(text)

bx.seq.seq_file(file, format=None, revcomp=False, name='', gap=None, contig=None)

bx.seq.seq_reader(file, format=None, revcomp=False, name='', gap=None)

bx.seq.seq_writer(outfile, format=None, name='')