Bio.SeqIO.NibIO module
Bio.SeqIO support for the UCSC nib file format.
Nib stands for nibble (4 bit) representation of nucleotide sequences. The two nibbles in a byte each store one nucleotide, represented numerically as follows:
0
- T
1
- C
2
- A
3
- G
4
- N (unknown)
As the first bit in a nibble is set if the nucleotide is soft-masked, we additionally have:
8
- t
9
- c
a
- a
b
- g
c
- n (unknown)
A nib file contains only one sequence record. You are expected to use this module via the Bio.SeqIO functions under the format name “nib”:
>>> from Bio import SeqIO
>>> record = SeqIO.read("Nib/test_even_bigendian.nib", "nib")
>>> print("%i %s..." % (len(record), record.seq[:20]))
50 nAGAAGagccgcNGgCActt...
For detailed information on the file format, please see the UCSC description at https://genome.ucsc.edu/FAQ/FAQformat.html.
- class Bio.SeqIO.NibIO.NibIterator(source)
Bases:
SequenceIterator
Parser for nib files.
- modes = 'b'
- __init__(source)
Iterate over a nib file and yield a SeqRecord.
source - a file-like object or a path to a file in the nib file format as defined by UCSC; the file must be opened in binary mode.
Note that a nib file always contains only one sequence record. The sequence of the resulting SeqRecord object should match the sequence generated by Jim Kent’s nibFrag utility run with the -masked option.
This function is used internally via the Bio.SeqIO functions:
>>> from Bio import SeqIO >>> record = SeqIO.read("Nib/test_even_bigendian.nib", "nib") >>> print("%s %i" % (record.seq, len(record))) nAGAAGagccgcNGgCActtGAnTAtCGTCgcCacCaGncGncTtGNtGG 50
You can also call it directly:
>>> with open("Nib/test_even_bigendian.nib", "rb") as handle: ... for record in NibIterator(handle): ... print("%s %i" % (record.seq, len(record))) ... nAGAAGagccgcNGgCActtGAnTAtCGTCgcCacCaGncGncTtGNtGG 50
- __next__()
Iterate over the records in the nib file.
- __abstractmethods__ = frozenset({})
- __parameters__ = ()
- class Bio.SeqIO.NibIO.NibWriter(target)
Bases:
SequenceWriter
Nib file writer.
- modes = 'b'
- __init__(target)
Initialize a Nib writer object.
- Arguments:
target - output stream opened in binary mode, or a path to a file
- write_header()
Write the file header.
- write_record(record)
Write a single record to the output file.
- write_records(records)
Write records to the output file, and return the number of records.
records - A list or iterator returning SeqRecord objects