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Support reading and writing to/from file-like objects #148

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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -18,3 +18,4 @@ _static
_templates
setup-requires/*
.cache/v/cache/lastfailed
.idea
136 changes: 91 additions & 45 deletions cyvcf2/cyvcf2.pyx
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,10 @@ import numpy as np
from array import array
import math
import ctypes

try:
from pathlib import Path
except ImportError:
from pathlib2 import Path # python 2 backport
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I suppose for python2 this makes pathlib or pathlib2 a dependency? Can we just not support python2 after a certain version of cyvcf2? It would make things so much nicer, especially if we can use the typing library for python 3?

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we need to keep python2 support.


from libc cimport stdlib
cimport numpy as np
Expand Down Expand Up @@ -130,7 +133,87 @@ cdef set_constants(VCF v):
v.HOM_ALT = 3


cdef class VCF:

cdef class HTSFile:

cdef htsFile *hts
cdef bytes fname
cdef bytes mode
cdef bint from_path
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there's probably more in VCF that's needed across both VCF and Writer that we can move here.


cdef _open_htsfile(self, fname, mode):
"""Opens an htsfile for reading or writing.

Parameters
----------
fname: str
filename (str or Path), file descriptor (int), or file-like object (has fileno method).
mode: str
the mode to pass to hts_open.
"""
cdef hFILE *hf
self.mode = to_bytes(mode)
reading = b"r" in self.mode
if not reading and not b"w":
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raise IOError("No 'r' or 'w' in mode %s" % str(self.mode))
self.from_path = False
# for htslib, wbu seems to not work
if mode == b"wbu":
mode = to_bytes(b"wb0")
if isinstance(fname, (basestring, Path)):
self.from_path = True
self.fname = to_bytes(str(fname))
if self.fname == b"-":
self.fname = to_bytes(b"/dev/stdin") if reading else to_bytes(b"/dev/stdout")
if self.fname.endswith(b".gz") and self.mode == b"w":
self.mode = b"wz"
elif self.fname.endswith(b".bcf") and self.mode == b"w":
self.mode = b"wb"
self.fname = to_bytes(str(fname))
self.mode = to_bytes(mode)
self.hts = hts_open(self.fname, self.mode)
# from a file descriptor
elif isinstance(fname, int):
self.mode = to_bytes(mode)
hf = hdopen(int(fname), self.mode)
self.hts = hts_hopen(hf, "<file>", self.mode)
self.fname = None
# reading from a File object or other object with fileno
elif hasattr(fname, "fileno"):
if fname.closed:
raise IOError('I/O operation on closed file')
self.mode = to_bytes(mode)
hf = hdopen(fname.fileno(), self.mode)
self.hts = hts_hopen(hf, "<file>", self.mode)
# .name can be TextIOWrapper
try:
self.fname = to_bytes(fname.name)
except AttributeError:
self.fname = None
else:
raise IOError("Cannot open '%s' for writing." % str(type(fname)))

if self.hts == NULL:
raise IOError("Error opening %s" % str(fname))
if reading:
if self.hts.format.format != vcf and self.hts.format.format != bcf:
raise IOError(
"%s if not valid bcf or vcf (format: %s mode: %s)" % (fname, self.hts.format.format, mode)
)
else:
if self.hts.format.format != text_format and self.hts.format.format != binary_format:
raise IOError(
"%s if not valid text_format or binary_format (format: %s mode: %s)" % (fname, self.hts.format.format, mode)
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)

def close(self):
if self.hts != NULL:
if self.from_path:
hts_close(self.hts)
self.hts = NULL


cdef class VCF(HTSFile):
"""
VCF class holds methods to iterate over and query a VCF.

Expand All @@ -146,20 +229,20 @@ cdef class VCF:
if True, then any '.' present in a genotype will classify the corresponding element in the gt_types array as UNKNOWN.
samples: list
list of samples to extract from full set in file.
threads: int
the number of threads to use including this reader.


Returns
-------
VCF object for iterating and querying.
"""

cdef htsFile *hts
cdef const bcf_hdr_t *hdr
cdef tbx_t *idx
cdef hts_idx_t *hidx
cdef int n_samples
cdef int PASS
cdef bytes fname
cdef bint gts012
cdef bint lazy
cdef bint strict_gt
Expand All @@ -178,25 +261,8 @@ cdef class VCF:
cdef readonly int UNKNOWN

def __init__(self, fname, mode="r", gts012=False, lazy=False, strict_gt=False, samples=None, threads=None):
cdef hFILE *hf

if isinstance(fname, basestring):
if fname == b"-" or fname == "-":
fname = b"/dev/stdin"
fname, mode = to_bytes(fname), to_bytes(mode)
self.hts = hts_open(fname, mode)
self.fname = fname
else:
mode = to_bytes(mode)
hf = hdopen(int(fname), mode)
self.hts = hts_hopen(hf, "<file>", mode)

if self.hts == NULL:
raise IOError("Error opening %s" % fname)
if self.hts.format.format != vcf and self.hts.format.format != bcf:
raise IOError("%s if not valid bcf or vcf" % fname)

cdef bcf_hdr_t *hdr
self._open_htsfile(fname, mode)
hdr = self.hdr = bcf_hdr_read(self.hts)
if samples is not None:
self.set_samples(samples)
Expand Down Expand Up @@ -491,13 +557,6 @@ cdef class VCF:

contains = __contains__

def close(self):
if self.hts != NULL:
if self.fname != "-":
# TODO flush
hts_close(self.hts)
self.hts = NULL

def __dealloc__(self):
if self.hts != NULL and self.hdr != NULL:
bcf_hdr_destroy(self.hdr)
Expand Down Expand Up @@ -2155,6 +2214,7 @@ cdef from_bytes(s):
return s


# TODO: make Writer extend HTSFile not VCF by moving common methods into HTSFile
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^this should be a tech-debt issue

cdef class Writer(VCF):
"""
Writer class makes a VCF Writer.
Expand All @@ -2177,15 +2237,7 @@ cdef class Writer(VCF):
cdef const bcf_hdr_t *ohdr

def __init__(Writer self, fname, VCF tmpl, mode="w"):
self.name = to_bytes(fname)
if fname.endswith(".gz") and mode == "w":
mode = "wz"
if fname.endswith(".bcf") and mode == "w":
mode = "wb"
self.hts = hts_open(self.name, to_bytes(mode))
if self.hts == NULL:
raise Exception("error opening file: %s" % self.name)

self._open_htsfile(fname, mode)
bcf_hdr_sync(tmpl.hdr)
self.ohdr = tmpl.hdr
self.hdr = bcf_hdr_dup(tmpl.hdr)
Expand All @@ -2195,14 +2247,8 @@ cdef class Writer(VCF):
@classmethod
def from_string(Writer cls, fname, header_string, mode="w"):
cdef Writer self = Writer.__new__(Writer)

self.name = to_bytes(fname)
if fname.endswith(".gz") and mode == "w":
mode = "wz"
if fname.endswith(".bcf") and mode == "w":
mode = "wb"
self.hts = hts_open(self.name, to_bytes(mode))
cdef char *hmode = "w"
self._open_htsfile(fname, mode)
self.hdr = bcf_hdr_init(hmode)
self.ohdr = bcf_hdr_dup(self.hdr)
if bcf_hdr_parse(self.hdr, to_bytes(header_string)) != 0:
Expand Down
68 changes: 54 additions & 14 deletions cyvcf2/tests/test_reader.py
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,11 @@
import sys
import os
import atexit
try:
from pathlib import Path
except ImportError:
from pathlib2 import Path # python 2 backport


HERE = os.path.dirname(__file__)
VCF_PATH = os.path.join(HERE, "test.vcf.gz")
Expand All @@ -20,8 +25,29 @@
basestring = (str, bytes)

def test_init():
# string
v = VCF(VCF_PATH)
assert v
expected_count = sum(1 for _ in v)
v.close()

# Path
v = VCF(Path(VCF_PATH))
value = sum(1 for _ in v)
assert value == expected_count

# file descriptor
with open(VCF_PATH) as fp:
fd = fp.fileno()
v = VCF(fd)
assert sum(1 for _ in v) == expected_count
v.close() # this should not close the file descriptor originally opened

# file-like object
with open(VCF_PATH) as fp:
v = VCF(fp)
assert sum(1 for _ in v) == expected_count
v.close() # this should not close the file descriptor originally opened

def test_type():
vcf = VCF(VCF_PATH)
Expand Down Expand Up @@ -237,32 +263,46 @@ def test_writer_from_string():
w.close()


def test_writer():

v = VCF(VCF_PATH)
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)

o = Writer(f, v)
rec = next(v)
def run_writer(writer, filename, rec):
rec.INFO["AC"] = "3"
rec.FILTER = ["LowQual"]
o.write_record(rec)
writer.write_record(rec)

rec.FILTER = ["LowQual", "VQSRTrancheSNP99.90to100.00"]
o.write_record(rec)

writer.write_record(rec)

rec.FILTER = "PASS"
o.write_record(rec)
writer.write_record(rec)

o.close()
writer.close()

expected = ["LowQual", "LowQual;VQSRTrancheSNP99.90to100.00", None]

for i, variant in enumerate(VCF(f)):
for i, variant in enumerate(VCF(filename)):
assert variant.FILTER == expected[i], (variant.FILTER, expected[i])

def test_writer():
v = VCF(VCF_PATH)
f = tempfile.mktemp(suffix=".vcf")
atexit.register(os.unlink, f)
rec = next(v)

# string
run_writer(Writer(f, v), f, rec)

# Path
path = Path(f)
run_writer(Writer(path, v), f, rec)

# file descriptor
with open(VCF_PATH) as fp:
fd = fp.fileno()
run_writer(Writer(fd, v), f, rec)

# file-like object
with open(VCF_PATH) as fp:
run_writer(Writer(fp, v), f, rec)
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I'm all ears for having a regression test for stdin/stdout support in the reader/writer, but I don't have a good solution


def test_add_info_to_header():
v = VCF(VCF_PATH)
v.add_info_to_header({'ID': 'abcdefg', 'Description': 'abcdefg',
Expand Down