bx.seq.nib module

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

class bx.seq.nib.NibFile(file, revcomp=False, name='', gap=None)

Bases: SeqFile

raw_fetch(start, length)

class bx.seq.nib.NibReader(file, revcomp=False, name='', gap=None)

Bases: SeqReader

class bx.seq.nib.NibWriter(file)

Bases: object

close()

write(seq)