class Bioconvert(object):
"""Universal converter used by the standalone
::
from bioconvert import Bioconvert
c = Bioconvert("test.fastq", "test.fasta", threads=4, force=True)
"""
def __init__(self, infile, outfile, force=False, threads=None, extra=None):
""".. rubric:: constructor
:param str infile: The path of the input file.
:param str outfile: The path of The output file
:param bool force: overwrite output file if it exists already
otherwise raises an error
"""
# don't check the input file because there are cases where input parameter is just a prefix
# if os.path.exists(infile) is False:
# msg = "Incorrect input file: %s" % infile
# _log.error(msg)
# raise ValueError(msg)
# check existence of output file. If it exists,
# fails except if force argument is set to True
if type(outfile) is str:
outfile = [outfile]
if type(infile) is str:
infile = [infile]
# some checking on the output files (existence, special case of dsrc)
for filename in outfile:
if os.path.exists(filename) is True:
msg = "output file {} exists already.".format(filename)
if force is False:
_log.critical(
"output file exists. If you are using bioconvert, use --force "
)
raise ValueError(msg)
else:
_log.warning(msg + " --force used so will be over written")
# Only fastq files can be compressed with dsrc
if filename.endswith(".dsrc"):
# only valid for FastQ files extension
# dsrc accepts only .fastq file extension
if filename.endswith(".fastq.dsrc") is False:
msg = "When compressing with .dsrc extension, " +\
"only files ending with .fastq extension are " +\
"accepted. This is due to the way dsrc executable "+\
"is implemented."
_log.critical(msg)
raise IOError
Lin = len(infile)
Lout = len(outfile)
self.inext = []
self.outext = []
# populate the inext
for filename in infile:
# example: fastq.gz to fasta.bz2
# Here, we want to decompress, convert, compress.
# so we need the extension without .gz or .bz2
# We should have inext set to fastq and outext
# set to fasta.bz2
self.inext.append(getext(filename, remove_compression=True))
# populate the outext
for filename in outfile:
self.outext.append(getext(filename, remove_compression=True))
# special case one to one for compression/decompression
# Case 2, fastq.gz to fastq.bz2
# data is not changed, just the type of compression, so we want
# to keep the original extensions, here inext and outext will contain
# .gz and .bz2
# if 1 to 1 and same extension, we overwrite self.inext and self.outext
if Lin == Lout == 1:
if self.inext == self.outext:
_log.info("decompression/compression mode")
self.inext = [getext(infile[0])]
self.outext = [getext(outfile[0])]
self.mapper = Registry()
# From the input parameters 1 and 2, we get the module name
if not list(
set(list(self.mapper.get_converters_names())).intersection(
sys.argv)):
# get format from extensions
in_fmt = [get_format_from_extension(x) for x in self.inext]
out_fmt = [get_format_from_extension(x) for x in self.outext]
else:
in_fmt, out_fmt = ConvMeta.split_converter_to_format(
list(
set(list(self.mapper.get_converters_names())).intersection(
sys.argv))[0])
self.in_fmt = in_fmt
self.out_fmt = out_fmt
self.in_fmt = [format.lower() for format in in_fmt]
self.in_fmt = tuple(in_fmt)
self.out_fmt = [format.lower() for format in out_fmt]
self.out_fmt = tuple(out_fmt)
_log.info("Input: {}".format(self.in_fmt))
_log.info("Output: {}".format(self.out_fmt))
try:
class_converter = self.mapper[(self.in_fmt, self.out_fmt)]
self.name = class_converter.__name__
except KeyError:
# This module name was not found
# Try to find path of converters
conv_path = self.mapper.conversion_path(self.in_fmt, self.out_fmt)
_log.debug("path: {}".format(conv_path))
if conv_path:
_log.info("Direct conversion not implemented. "
"Chaining converters.")
# implemented in bioconvert/core/base.py
# using temporary files
class_converter = make_chain([(pair, self.mapper[pair])
for pair in conv_path])
else:
msg = "Requested input format ('{}') to output format ('{}') is not available in bioconvert".format(
self.in_fmt,
self.out_fmt,
)
_log.critical(msg)
_log.critical(
"Use --formats to know the available formats and --help for examples"
)
raise Exception(msg)
# If --threads provided, we update the threads attribute
#FIXME: hack for the compression/decompression decorators
if Lin == 1:
infile = infile[0]
if Lout == 1:
outfile = outfile[0]
self.converter = class_converter(infile, outfile)
if threads is not None:
self.converter.threads = threads
if extra:
self.converter._extra_arguments = extra
_log.info("Using {} class (with {} threads if needed)".format(
self.converter.name, self.converter.threads))
def __call__(self, *args, **kwargs):
self.converter(*args, **kwargs)
def boxplot_benchmark(self, *args, **kwargs):
self.converter.boxplot_benchmark(*args, **kwargs)
class Bioconvert(object):
"""Universal converter used by the standalone
::
from bioconvert import Bioconvert
c = Bioconvert("test.fastq", "test.fasta")
"""
def __init__(self, infile, outfile, in_fmt=None, out_fmt=None, force=False):
""".. rubric:: constructor
:param str infile: The path of the input file.
:param str outfile: The path of The output file
:param str in_fmt: the format for the input file
:param str out_fmt: the format for the output
:param bool force: overwrite output file if it exists already
otherwise raises an error
"""
# don't check the input file because there are cases where input parameter is just a prefix
# if os.path.exists(infile) is False:
# msg = "Incorrect input file: %s" % infile
# _log.error(msg)
# raise ValueError(msg)
# check existence of output file. If it exists,
# fails except if force argument is set to True
if os.path.exists(outfile) is True:
msg = "output file {} exists already".format(outfile)
_log.warning("output file exists already")
if force is False:
_log.critical("output file exists. If you are using bioconvert, use --force ")
raise ValueError(msg)
else:
_log.warning("output file will be overwritten")
# Only fastq files can be compressed with dsrc
if outfile.endswith(".dsrc"):
# only valid for FastQ files extension
# dsrc accepts only .fastq file extension
if outfile.endswith(".fastq.dsrc") is False:
msg = "When compressing with .dsrc extension, " +\
"only files ending with .fastq extension are " +\
"accepted. This is due to the way dsrc executable +"\
"is implemented."
_log.critical(msg)
raise IOError
# Case1: fastq.gz to fasta.bz2
# Here, we want to decompress, convert, compress.
# so we need the extension without .gz or .bz2
# We should have inext set to fastq and outext
# set to fasta.bz2
self.inext = getext(infile, remove_compression=True)
self.outext = getext(outfile, remove_compression=True)
# Case 2, fastq.gz to fastq.bz2
# data is not changed, just the type of compression, so we want
# to keep the original extensions, here inext and outext will contain
# .gz and .bz2
if self.inext == self.outext:
_log.info("decompression/compression mode")
self.inext = getext(infile)
self.outext = getext(outfile)
self.mapper = Registry()
# From the input parameters 1 and 2, we get the module name
try:
if in_fmt is None:
in_fmt = get_format_from_extension(self.inext)
if out_fmt is None:
out_fmt = get_format_from_extension(self.outext)
self.in_fmt = in_fmt.upper()
self.out_fmt = out_fmt.upper()
_log.info("Input: %s", self.in_fmt)
_log.info("Output: %s", self.out_fmt)
class_converter = self.mapper[(self.in_fmt, self.out_fmt)]
self.name = class_converter.__name__
except KeyError:
# This module name was not found
# Try to find path of converters
conv_path = self.mapper.conversion_path(self.in_fmt, self.out_fmt)
_log.debug("path: {}".format(conv_path))
if conv_path:
_log.info("Direct conversion not implemented. "
"Chaining converters.")
# implemented in bioconvert/core/base.py
# using temporary files
class_converter = make_chain([
(pair, self.mapper[pair]) for pair in conv_path])
else:
msg = "Requested input format ('%s') to output format ('%s') is not available in bioconvert" %(
self.in_fmt,
self.out_fmt,
)
_log.critical(msg)
_log.critical("Use --formats to know the available formats and --help for examples")
raise Exception(msg)
self.converter = class_converter(infile, outfile)
_log.info("Using {} class".format(self.converter.name))
def __call__(self, *args, **kwargs):
self.converter(*args, **kwargs)
def boxplot_benchmark(self, *args, **kwargs):
self.converter.boxplot_benchmark(*args, **kwargs)
