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import sys
import os
import pysam
import difflib
import gzip
import inspect
import tempfile
IS_PYTHON3 = sys.version_info[0] >= 3
if IS_PYTHON3:
from itertools import zip_longest
from urllib.request import urlopen
else:
from itertools import izip as zip_longest
from urllib2 import urlopen
if IS_PYTHON3:
def force_str(s):
try:
return s.decode('ascii')
except AttributeError:
return s
def force_bytes(s):
try:
return s.encode('ascii')
except AttributeError:
return s
else:
def force_str(s):
return s
def force_bytes(s):
return s
def openfile(fn):
if fn.endswith(".gz"):
try:
return gzip.open(fn, "rt", encoding="utf-8")
except TypeError:
return gzip.open(fn, "r")
else:
return open(fn)
def checkBinaryEqual(filename1, filename2):
'''return true if the two files are binary equal.
'''
if os.path.getsize(filename1) != os.path.getsize(filename2):
return False
infile1 = open(filename1, "rb")
infile2 = open(filename2, "rb")
def chariter(infile):
while 1:
c = infile.read(1)
if c == b"":
break
yield c
found = False
for c1, c2 in zip_longest(chariter(infile1), chariter(infile2)):
if c1 != c2:
break
else:
found = True
infile1.close()
infile2.close()
return found
def check_samtools_view_equal(
filename1, filename2,
without_header=False):
'''return true if the two files are equal in their
content through samtools view.
'''
# strip MD and NM tags, as not preserved in CRAM files
args = ["-x", "MD", "-x", "NM"]
if not without_header:
args.append("-h")
lines1 = pysam.samtools.view(*(args + [filename1]))
lines2 = pysam.samtools.view(*(args + [filename2]))
if len(lines1) != len(lines2):
return False
if lines1 != lines2:
# line by line comparison
# sort each line, as tags get rearranged between
# BAM/CRAM
for n, pair in enumerate(zip(lines1, lines2)):
l1, l2 = pair
l1 = sorted(l1[:-1].split("\t"))
l2 = sorted(l2[:-1].split("\t"))
if l1 != l2:
print ("mismatch in line %i" % n)
print (l1)
print (l2)
return False
else:
return False
return True
def checkURL(url):
'''return True if URL is available.
A URL might not be available if it is the wrong URL
or there is no connection to the URL.
'''
try:
urlopen(url, timeout=1)
return True
except:
return False
def checkFieldEqual(cls, read1, read2, exclude=[]):
'''check if two reads are equal by comparing each field.'''
# add the . for refactoring purposes.
for x in (".query_name",
".query_sequence",
".flag",
".reference_id",
".reference_start",
".mapping_quality",
".cigartuples",
".next_reference_id",
".next_reference_start",
".template_length",
".query_length",
".query_qualities",
".bin",
".is_paired", ".is_proper_pair",
".is_unmapped", ".mate_is_unmapped",
".is_reverse", ".mate_is_reverse",
".is_read1", ".is_read2",
".is_secondary", ".is_qcfail",
".is_duplicate"):
n = x[1:]
if n in exclude:
continue
cls.assertEqual(getattr(read1, n), getattr(read2, n),
"attribute mismatch for %s: %s != %s" %
(n, getattr(read1, n), getattr(read2, n)))
def check_lines_equal(cls, a, b, sort=False, filter_f=None, msg=None):
"""check if contents of two files are equal comparing line-wise.
sort: bool
sort contents of both files before comparing.
filter_f:
remover lines in both a and b where expression is True
"""
aa = openfile(a).readlines()
bb = openfile(b).readlines()
if filter_f is not None:
aa = [x for x in aa if not filter_f(x)]
bb = [x for x in bb if not filter_f(x)]
if sort:
cls.assertEqual(sorted(aa), sorted(bb), msg)
else:
cls.assertEqual(aa, bb, msg)
def get_temp_filename(suffix=""):
caller_name = inspect.getouterframes(inspect.currentframe(), 2)[1][3]
f = tempfile.NamedTemporaryFile(
prefix="tmp_{}_".format(caller_name),
suffix=suffix,
delete=False,
dir=".")
f.close()
return f.name
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