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implement tabix region query natively in python #297

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7e6cc16
implement tabix region query natively
Jan 7, 2020
8e33fcd
fix flake8 check failed
Jan 7, 2020
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142 changes: 61 additions & 81 deletions allel/io/vcf_read.py
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@
from collections import namedtuple, defaultdict
import warnings
import time
import subprocess
import textwrap
from collections import OrderedDict
from allel.io.vcfreader import VCFReader


import numpy as np
Expand Down Expand Up @@ -205,11 +205,12 @@ def _chunk_iter_rename(it, rename_fields):
overlaps the region - such a variant will *not* be included in the data
returned by this function."""

_doc_param_tabix = \
"""Name or path to tabix executable. Only required if `region` is given. Setting
`tabix` to `None` will cause a fall-back to scanning through the VCF file from
the beginning, which may be much slower than tabix but the only option if tabix
is not available on your system and/or the VCF file has not been tabix-indexed."""
_doc_param_index = \
"""Path to the index file of the VCF. Only required if `region` is given. Setting to `None` (the
default) will automatically check weather there is a index file with the same name but
suffix '.tbi', which is the most common case. A warning will be issued if the index file
is older than the VCF file.
"""

_doc_param_samples = \
"""Selection of samples to extract calldata for. If provided, should be a list of
Expand Down Expand Up @@ -244,7 +245,7 @@ def read_vcf(input,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
index=None,
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
Expand Down Expand Up @@ -276,8 +277,8 @@ def read_vcf(input,
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
index : string, optional
{index}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
Expand All @@ -304,7 +305,7 @@ def read_vcf(input,
fields, samples, headers, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
chunk_length=chunk_length, fills=fills, region=region, index=index,
samples=samples, transformers=transformers
)

Expand Down Expand Up @@ -353,7 +354,7 @@ def read_vcf(input,
alt_number=_doc_param_alt_number,
fills=_doc_param_fills,
region=_doc_param_region,
tabix=_doc_param_tabix,
index=_doc_param_index,
samples=_doc_param_samples,
transformers=_doc_param_transformers,
buffer_size=_doc_param_buffer_size,
Expand Down Expand Up @@ -381,7 +382,7 @@ def vcf_to_npz(input, output,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix=True,
index=None,
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
Expand Down Expand Up @@ -419,8 +420,8 @@ def vcf_to_npz(input, output,
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
index : string, optional
{index}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
Expand All @@ -443,7 +444,7 @@ def vcf_to_npz(input, output,
input=input, fields=fields, exclude_fields=exclude_fields,
rename_fields=rename_fields, types=types, numbers=numbers,
alt_number=alt_number, buffer_size=buffer_size, chunk_length=chunk_length,
log=log, fills=fills, region=region, tabix=tabix, samples=samples,
log=log, fills=fills, region=region, index=index, samples=samples,
transformers=transformers
)

Expand Down Expand Up @@ -473,7 +474,7 @@ def vcf_to_npz(input, output,
alt_number=_doc_param_alt_number,
fills=_doc_param_fills,
region=_doc_param_region,
tabix=_doc_param_tabix,
index=_doc_param_index,
samples=_doc_param_samples,
transformers=_doc_param_transformers,
buffer_size=_doc_param_buffer_size,
Expand Down Expand Up @@ -610,7 +611,7 @@ def vcf_to_hdf5(input, output,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
index=None,
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
Expand Down Expand Up @@ -666,8 +667,8 @@ def vcf_to_hdf5(input, output,
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
index : string, optional
{index}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
Expand All @@ -693,7 +694,7 @@ def vcf_to_hdf5(input, output,
fields, samples, headers, it = iter_vcf_chunks(
input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
chunk_length=chunk_length, fills=fills, region=region, index=index,
samples=samples, transformers=transformers
)

Expand Down Expand Up @@ -767,7 +768,7 @@ def vcf_to_hdf5(input, output,
alt_number=_doc_param_alt_number,
fills=_doc_param_fills,
region=_doc_param_region,
tabix=_doc_param_tabix,
index=_doc_param_index,
samples=_doc_param_samples,
transformers=_doc_param_transformers,
buffer_size=_doc_param_buffer_size,
Expand Down Expand Up @@ -850,7 +851,7 @@ def vcf_to_zarr(input, output,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
index=None,
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
Expand Down Expand Up @@ -891,8 +892,8 @@ def vcf_to_zarr(input, output,
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
index : string, optional
{index}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
Expand All @@ -918,7 +919,7 @@ def vcf_to_zarr(input, output,
fields, samples, headers, it = iter_vcf_chunks(
input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix,
chunk_length=chunk_length, fills=fills, region=region, index=index,
samples=samples, transformers=transformers
)

Expand Down Expand Up @@ -997,7 +998,7 @@ def vcf_to_zarr(input, output,
alt_number=_doc_param_alt_number,
fills=_doc_param_fills,
region=_doc_param_region,
tabix=_doc_param_tabix,
index=_doc_param_index,
samples=_doc_param_samples,
transformers=_doc_param_transformers,
buffer_size=_doc_param_buffer_size,
Expand All @@ -1008,46 +1009,25 @@ def vcf_to_zarr(input, output,


# noinspection PyShadowingBuiltins
def _setup_input_stream(input, region=None, tabix=None, buffer_size=DEFAULT_BUFFER_SIZE):
def _setup_input_stream(input, index=None, region=None, buffer_size=DEFAULT_BUFFER_SIZE):

# obtain a file-like object
close = False
if isinstance(input, str) and input.endswith('gz'):
if index is None:
index_file = '{}.tbi'.format(input)
if os.path.exists(index_file):
index = index_file

if region and tabix and os.name != 'nt':

try:
# try tabix
p = subprocess.Popen([tabix, '-h', input, region],
stdout=subprocess.PIPE,
stderr=subprocess.STDOUT,
bufsize=0)

# check if tabix exited early, look for tabix error
time.sleep(.5)
poll = p.poll()
if poll is not None and poll > 0:
err = p.stdout.read()
err = str(err, 'ascii')
p.stdout.close()
raise RuntimeError(err.strip())
fileobj = p.stdout
close = True
# N.B., still pass the region parameter through so we get strictly only
# variants that start within the requested region. See also
# https://github.com/alimanfoo/vcfnp/issues/54

except FileNotFoundError:
# no tabix, fall back to scanning
warnings.warn('tabix not found, falling back to scanning to region')
fileobj = gzip.open(input, mode='rb')
close = True

except Exception as e:
warnings.warn('error occurred attempting tabix (%s); falling back to '
'scanning to region' % e)
fileobj = gzip.open(input, mode='rb')
close = True
if index is not None and os.path.getmtime(index) < os.path.getmtime(input):
warnings.warn('the index file is older than the input VCF: {}'.format(index))

if region and index is not None:
fileobj = VCFReader(input, index, region) # random access
close = True
# N.B., still pass the region parameter through so we get strictly only
# variants that start within the requested region. See also
# https://github.com/alimanfoo/vcfnp/issues/54

else:
fileobj = gzip.open(input, mode='rb')
Expand Down Expand Up @@ -1076,7 +1056,7 @@ def iter_vcf_chunks(input,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
index=None,
samples=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
Expand All @@ -1101,8 +1081,8 @@ def iter_vcf_chunks(input,
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
index : string, optional
{index}
samples : list of strings
{samples}
transformers : list of transformer objects, optional
Expand Down Expand Up @@ -1131,7 +1111,7 @@ def iter_vcf_chunks(input,
fills=fills, samples=samples, region=region)

# setup input stream
stream = _setup_input_stream(input=input, region=region, tabix=tabix,
stream = _setup_input_stream(input=input, index=index, region=region, # tabix=tabix,
buffer_size=buffer_size)

# setup iterator
Expand All @@ -1158,7 +1138,7 @@ def iter_vcf_chunks(input,
alt_number=_doc_param_alt_number,
fills=_doc_param_fills,
region=_doc_param_region,
tabix=_doc_param_tabix,
index=_doc_param_index,
samples=_doc_param_samples,
transformers=_doc_param_transformers,
buffer_size=_doc_param_buffer_size,
Expand Down Expand Up @@ -1797,7 +1777,7 @@ def vcf_to_dataframe(input,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
index=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
Expand All @@ -1822,8 +1802,8 @@ def vcf_to_dataframe(input,
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
index : string, optional
{index}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
Expand All @@ -1849,7 +1829,7 @@ def vcf_to_dataframe(input,
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
chunk_length=chunk_length, fills=fills, region=region, index=index, samples=[],
transformers=transformers
)

Expand Down Expand Up @@ -1881,7 +1861,7 @@ def vcf_to_dataframe(input,
alt_number=_doc_param_alt_number,
fills=_doc_param_fills,
region=_doc_param_region,
tabix=_doc_param_tabix,
index=_doc_param_index,
transformers=_doc_param_transformers,
buffer_size=_doc_param_buffer_size,
chunk_length=_doc_param_chunk_length,
Expand All @@ -1898,7 +1878,7 @@ def vcf_to_csv(input, output,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
index=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
Expand Down Expand Up @@ -1926,8 +1906,8 @@ def vcf_to_csv(input, output,
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
index : string, optional
{index}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
Expand All @@ -1950,7 +1930,7 @@ def vcf_to_csv(input, output,
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
chunk_length=chunk_length, fills=fills, region=region, index=index, samples=[],
transformers=transformers
)

Expand Down Expand Up @@ -1980,7 +1960,7 @@ def vcf_to_csv(input, output,
alt_number=_doc_param_alt_number,
fills=_doc_param_fills,
region=_doc_param_region,
tabix=_doc_param_tabix,
index=_doc_param_index,
transformers=_doc_param_transformers,
buffer_size=_doc_param_buffer_size,
chunk_length=_doc_param_chunk_length,
Expand Down Expand Up @@ -2016,7 +1996,7 @@ def vcf_to_recarray(input,
alt_number=DEFAULT_ALT_NUMBER,
fills=None,
region=None,
tabix='tabix',
index=None,
transformers=None,
buffer_size=DEFAULT_BUFFER_SIZE,
chunk_length=DEFAULT_CHUNK_LENGTH,
Expand All @@ -2041,8 +2021,8 @@ def vcf_to_recarray(input,
{fills}
region : string, optional
{region}
tabix : string, optional
{tabix}
index : string, optional
{index}
transformers : list of transformer objects, optional
{transformers}
buffer_size : int, optional
Expand All @@ -2067,7 +2047,7 @@ def vcf_to_recarray(input,
fields, _, _, it = iter_vcf_chunks(
input=input, fields=fields, exclude_fields=exclude_fields, types=types,
numbers=numbers, alt_number=alt_number, buffer_size=buffer_size,
chunk_length=chunk_length, fills=fills, region=region, tabix=tabix, samples=[],
chunk_length=chunk_length, fills=fills, region=region, index=index, samples=[],
transformers=transformers
)

Expand Down Expand Up @@ -2098,7 +2078,7 @@ def vcf_to_recarray(input,
alt_number=_doc_param_alt_number,
fills=_doc_param_fills,
region=_doc_param_region,
tabix=_doc_param_tabix,
index=_doc_param_index,
transformers=_doc_param_transformers,
buffer_size=_doc_param_buffer_size,
chunk_length=_doc_param_chunk_length,
Expand Down
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