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.
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class
Bio.SeqIO.NibIO.
NibIterator
(source)¶ Bases:
Bio.SeqIO.Interfaces.SequenceIterator
Parser for nib files.
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__init__
(self, 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
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parse
(self, handle)¶ Start parsing the file, and return a SeqRecord generator.
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iterate
(self, handle, byteorder)¶ Iterate over the records in the nib file.
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__abstractmethods__
= frozenset({})¶
-
-
class
Bio.SeqIO.NibIO.
NibWriter
(target)¶ Bases:
Bio.SeqIO.Interfaces.SequenceWriter
Nib file writer.
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__init__
(self, target)¶ Initialize a Nib writer object.
- Arguments:
target - output stream opened in binary mode, or a path to a file
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write_header
(self)¶ Write the file header.
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write_record
(self, record)¶ Write a single record to the output file.
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write_file
(self, records)¶ Write the complete file with the records, and return the number of records.
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