from pathlib import PurePath
import os
from .indexed_bam import IndexedBamFile
from .indexed_fasta import IndexedFasta, create_index
from .files import bnp_open
from .delimited_buffers import DelimitedBuffer
from .multiline_buffer import FastaIdx
class IndexBuffer(DelimitedBuffer):
sep = "\t"
dataclass = FastaIdx
[docs]
def open_indexed(filename: str) -> IndexedFasta:
"""Open an indexed fasta (for now) file with random access
If an index is not already present for the file, create it
Parameters
----------
filename : str
The filename of the file
Returns
-------
IndexedFasta
An Indexed fasta object that supports random access on
chromosome or intervals
Examples
--------
>>> from bionumpy import open_indexed
>>> reference = open_indexed("example_data/small_genome.fa")
>>> reference
Indexed Fasta File with chromosome sizes: {'0': 80, '1': 80, '2': 80, '3': 80}
>>> reference["1"]
encoded_array('gcttggtatgaaaacccatc...')
>>> from bionumpy.datatypes import Interval
>>> intervals = Interval.from_entry_tuples([("1", 10, 20), ("2", 20, 30)])
>>> reference.get_interval_sequences(intervals)
encoded_ragged_array(['aaaacccatc',
'ggccgttttt'])
"""
path = PurePath(filename)
suffix = path.suffixes[-1]
index_file_name = path.with_suffix(path.suffix + ".fai")
if suffix in (".fa", ".fasta"):
if not os.path.isfile(index_file_name):
index = create_index(path)
bnp_open(index_file_name, "w", buffer_type=IndexBuffer).write(index)
return IndexedFasta(filename)
elif suffix == '.bam':
return IndexedBamFile(filename, create_index=True)
else:
raise ValueError(f"Unknown file type {suffix} for indexed read. Only .fa, .fasta and .bam are supported.")