def _bzip_gzip(in_file):
"""
convert from bz2 to gz
"""
base, first_ext = os.path.splitext(in_file)
gzipped_file = base + ".gz"
if not file_exists(gzipped_file):
return gzipped_file
if (fastq.is_fastq(base) and utils.is_bzipped(in_file)
and not objectstore.is_remote(in_file)):
if file_exists(gzipped_file):
return gzipped_file
message = "gzipping {in_file}.".format(in_file=in_file)
do.run("bunzip2 -c {in_file} | gzip > {gzipped_file}".format(**locals()), message)
return gzipped_file
return in_file
def _gzip_fastq(in_file):
"""
gzip a fastq file if it is not already gzipped, handling conversion
from bzip to gzipped files
"""
if fastq.is_fastq(in_file) and not objectstore.is_remote(in_file):
if utils.is_bzipped(in_file):
return _bzip_gzip(in_file)
elif not utils.is_gzipped(in_file):
gzipped_file = in_file + ".gz"
if file_exists(gzipped_file):
return gzipped_file
message = "gzipping {in_file}.".format(in_file=in_file)
with file_transaction(gzipped_file) as tx_gzipped_file:
do.run("gzip -c {in_file} > {tx_gzipped_file}".format(**locals()),
message)
return gzipped_file
return in_file
def _bzip_gzip(in_file):
"""
convert from bz2 to gz
"""
if not utils.is_bzipped(in_file):
return in_file
base, first_ext = os.path.splitext(in_file)
gzipped_file = base + ".gz"
if (fastq.is_fastq(base) and
not objectstore.is_remote(in_file)):
if file_exists(gzipped_file):
return gzipped_file
message = "gzipping {in_file}.".format(in_file=in_file)
with file_transaction(gzipped_file) as tx_gzipped_file:
do.run("bunzip2 -c {in_file} | gzip > {tx_gzipped_file}".format(**locals()), message)
return gzipped_file
return in_file
def _gzip_fastq(in_file):
"""
gzip a fastq file if it is not already gzipped, handling conversion
from bzip to gzipped files
"""
if fastq.is_fastq(in_file) and not objectstore.is_remote(in_file):
if utils.is_bzipped(in_file):
return _bzip_gzip(in_file)
elif not utils.is_gzipped(in_file):
gzipped_file = in_file + ".gz"
if file_exists(gzipped_file):
return gzipped_file
message = "gzipping {in_file}.".format(in_file=in_file)
with file_transaction(gzipped_file) as tx_gzipped_file:
do.run("gzip -c {in_file} > {tx_gzipped_file}".format(**locals()),
message)
return gzipped_file
return in_file
def _bzip_gzip(in_file, out_dir=None):
"""
convert from bz2 to gz
"""
if not utils.is_bzipped(in_file):
return in_file
base, _ = os.path.splitext(in_file)
if out_dir:
gzipped_file = os.path.join(out_dir, os.path.basename(base) + ".gz")
else:
gzipped_file = base + ".gz"
if (fastq.is_fastq(base) and not objectstore.is_remote(in_file)):
if file_exists(gzipped_file):
return gzipped_file
message = "gzipping {in_file} to {gzipped_file}.".format(
in_file=in_file, gzipped_file=gzipped_file)
with file_transaction(gzipped_file) as tx_gzipped_file:
do.run("bunzip2 -c {in_file} | gzip > {tx_gzipped_file}".format(**locals()), message)
return gzipped_file
return in_file
def _bzip_gzip(in_file, out_dir=None):
"""
convert from bz2 to gz
"""
if not utils.is_bzipped(in_file):
return in_file
base, _ = os.path.splitext(in_file)
if out_dir:
gzipped_file = os.path.join(out_dir, os.path.basename(base) + ".gz")
else:
gzipped_file = base + ".gz"
if (fastq.is_fastq(base) and not objectstore.is_remote(in_file)):
if file_exists(gzipped_file):
return gzipped_file
message = "gzipping {in_file} to {gzipped_file}.".format(
in_file=in_file, gzipped_file=gzipped_file)
with file_transaction(gzipped_file) as tx_gzipped_file:
do.run("bunzip2 -c {in_file} | gzip > {tx_gzipped_file}".format(**locals()), message)
return gzipped_file
return in_file