Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Avoid a Python 3.10 regression in iterating GzipFiles #71

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Avoid a Python 3.10 regression in iterating GzipFiles #71

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
125 changes: 65 additions & 60 deletions test/test_oldindex.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -36,45 +36,48 @@
def get_header(filename, meta_char='#'):
"""Read gzipped file and retrieve lines beginning with '#'."""
retval = []
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith(meta_char):
retval.append(line.rstrip())
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith(meta_char):
retval.append(line.rstrip())
return retval


def get_chromsize(filename):
"""Read gzipped file and retrieve chromsize."""
retval = []
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith('#chromsize: '):
fields = line.rstrip().split('\s+')
chrname = fields[1]
chrsize = fields[2]
retval.append([chrname, chrsize])
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith('#chromsize: '):
fields = line.rstrip().split('\s+')
chrname = fields[1]
chrsize = fields[2]
retval.append([chrname, chrsize])
return retval


def read_vcf(filename):
"""Read a VCF file and return a list of [chrom, start, end] items."""
retval = []
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
fields = line.rstrip().split('\t')
chrom = fields[0]
start = fields[1]
end = fields[1]
retval.append([chrom, start, end])
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
fields = line.rstrip().split('\t')
chrom = fields[0]
start = fields[1]
end = fields[1]
retval.append([chrom, start, end])
return retval


Expand All @@ -83,20 +86,21 @@ def find_pairs_type(filename, delimiter='\t'):
or undetermined. Do this by testing string values of """
is_juicer = False
is_4DN = False
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
fields = line.rstrip().split(delimiter)
if len(fields)>=6 and is_str(fields[2]) and is_str(fields[6]):
is_juicer = True
if is_str(fields[2]) and is_str(fields[4]):
is_4DN = True
if not is_juicer and is_4DN:
return '4DN'
elif is_juicer:
return 'juicer'
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
fields = line.rstrip().split(delimiter)
if len(fields)>=6 and is_str(fields[2]) and is_str(fields[6]):
is_juicer = True
if is_str(fields[2]) and is_str(fields[4]):
is_4DN = True
if not is_juicer and is_4DN:
return '4DN'
elif is_juicer:
return 'juicer'
return 'undetermined'


Expand All @@ -115,25 +119,26 @@ def read_pairs(filename, file_type='undetermined', delimiter='\t'):
if file_type == 'undetermined':
return []
retval = []
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith('#'):
continue
fields = line.rstrip().split(delimiter)
if file_type == 'juicer':
chrom1 = fields[1]
start1 = fields[2]
chrom2 = fields[5]
start2 = fields[6]
elif file_type == '4DN':
chrom1 = fields[1]
start1 = fields[2]
chrom2 = fields[3]
start2 = fields[4]
retval.append([chrom1, start1, start1, chrom2, start2, start2])
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith('#'):
continue
fields = line.rstrip().split(delimiter)
if file_type == 'juicer':
chrom1 = fields[1]
start1 = fields[2]
chrom2 = fields[5]
start2 = fields[6]
elif file_type == '4DN':
chrom1 = fields[1]
start1 = fields[2]
chrom2 = fields[3]
start2 = fields[4]
retval.append([chrom1, start1, start1, chrom2, start2, start2])
return retval


Expand Down
125 changes: 65 additions & 60 deletions test/test_oldindex2.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -35,45 +35,48 @@
def get_header(filename, meta_char='#'):
"""Read gzipped file and retrieve lines beginning with '#'."""
retval = []
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith(meta_char):
retval.append(line.rstrip())
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith(meta_char):
retval.append(line.rstrip())
return retval


def get_chromsize(filename):
"""Read gzipped file and retrieve chromsize."""
retval = []
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith('#chromsize: '):
fields = line.rstrip().split('\s+')
chrname = fields[1]
chrsize = fields[2]
retval.append([chrname, chrsize])
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith('#chromsize: '):
fields = line.rstrip().split('\s+')
chrname = fields[1]
chrsize = fields[2]
retval.append([chrname, chrsize])
return retval


def read_vcf(filename):
"""Read a VCF file and return a list of [chrom, start, end] items."""
retval = []
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
fields = line.rstrip().split('\t')
chrom = fields[0]
start = fields[1]
end = fields[1]
retval.append([chrom, start, end])
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
fields = line.rstrip().split('\t')
chrom = fields[0]
start = fields[1]
end = fields[1]
retval.append([chrom, start, end])
return retval


Expand All @@ -82,20 +85,21 @@ def find_pairs_type(filename, delimiter='\t'):
or undetermined. Do this by testing string values of """
is_juicer = False
is_4DN = False
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
fields = line.rstrip().split(delimiter)
if len(fields)>=6 and is_str(fields[2]) and is_str(fields[6]):
is_juicer = True
if is_str(fields[2]) and is_str(fields[4]):
is_4DN = True
if not is_juicer and is_4DN:
return '4DN'
elif is_juicer:
return 'juicer'
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
fields = line.rstrip().split(delimiter)
if len(fields)>=6 and is_str(fields[2]) and is_str(fields[6]):
is_juicer = True
if is_str(fields[2]) and is_str(fields[4]):
is_4DN = True
if not is_juicer and is_4DN:
return '4DN'
elif is_juicer:
return 'juicer'
return 'undetermined'


Expand All @@ -114,25 +118,26 @@ def read_pairs(filename, file_type='undetermined', delimiter='\t'):
if file_type == 'undetermined':
return []
retval = []
for line in gzip.open(filename):
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith('#'):
continue
fields = line.rstrip().split(delimiter)
if file_type == 'juicer':
chrom1 = fields[1]
start1 = fields[2]
chrom2 = fields[5]
start2 = fields[6]
elif file_type == '4DN':
chrom1 = fields[1]
start1 = fields[2]
chrom2 = fields[3]
start2 = fields[4]
retval.append([chrom1, start1, start1, chrom2, start2, start2])
with gzip.open(filename) as f:
for line in f:
try:
line = line.decode('utf-8')
except AttributeError:
pass
if line.startswith('#'):
continue
fields = line.rstrip().split(delimiter)
if file_type == 'juicer':
chrom1 = fields[1]
start1 = fields[2]
chrom2 = fields[5]
start2 = fields[6]
elif file_type == '4DN':
chrom1 = fields[1]
start1 = fields[2]
chrom2 = fields[3]
start2 = fields[4]
retval.append([chrom1, start1, start1, chrom2, start2, start2])
return retval


Expand Down