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"""
Classes to support nib files.
:Author: James Taylor (james@bx.psu.edu), Bob Harris (rsharris@bx.psu.edu)
A nib sequence is a sequence of DNA, using the 10 character alphabet A,C,G,T,N
(upper and lower case). The file is packed as 4 bits per character.
nib file format
---------------
Fields can be in big- or little-endian format; they must match the endianess
of the magic number.
============ =========== ======================================================
offset 0x00: 6B E9 3D 3A big endian magic number (3A 3D E9 6B => little endian)
offset 0x04: xx xx xx xx length of data sequence (counted in characters)
offset 0x08: ... data sequence; most significant nybble in each
byte is first in sequence
============ =========== ======================================================
"""
import math
import struct
from bx.seq.seq import (
SeqFile,
SeqReader,
)
from . import _nib
NIB_MAGIC_NUMBER = 0x6BE93D3A
NIB_MAGIC_NUMBER_SWAP = 0x3A3DE96B
NIB_MAGIC_SIZE = 4
NIB_LENGTH_SIZE = 4
class NibFile(SeqFile):
def __init__(self, file, revcomp=False, name="", gap=None):
SeqFile.__init__(self, file, revcomp, name, gap)
self.byte_order = ">"
magic = struct.unpack(">L", file.read(NIB_MAGIC_SIZE))[0]
if magic != NIB_MAGIC_NUMBER:
if magic == NIB_MAGIC_NUMBER_SWAP:
self.byte_order = "<"
else:
raise Exception("Not a NIB file")
self.magic = magic
self.length = struct.unpack(f"{self.byte_order}L", file.read(NIB_LENGTH_SIZE))[0]
def raw_fetch(self, start, length):
# Check parameters
assert start >= 0, "Start must be greater than 0"
assert length >= 0, "Length must be greater than 0"
assert start + length <= self.length, "Interval beyond end of sequence"
# Read block of bytes containing sequence
block_start = int(math.floor(start / 2))
block_end = int(math.floor((start + length - 1) / 2))
block_len = block_end + 1 - block_start
self.file.seek(NIB_MAGIC_SIZE + NIB_LENGTH_SIZE + block_start)
raw = self.file.read(block_len)
# Unpack compressed block into a character string and return
return _nib.translate_raw_data(raw, start, length)
class NibReader(SeqReader):
def __init__(self, file, revcomp=False, name="", gap=None):
SeqReader.__init__(self, file, revcomp, name, gap)
def __next__(self):
if self.seqs_read != 0:
return # nib files have just one sequence
seq = NibFile(self.file, self.revcomp, self.name, self.gap)
self.seqs_read += 1
return seq
class NibWriter:
def __init__(self, file):
self.file = file
def write(self, seq):
assert False, "NibWriter.write() is not implemented yet"
def close(self):
self.file.close()
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