def bamdiff(pair, out_prefix=None):
"""
takes two coordinate sorted BAM files and outputs only the records unique
to each one. requires bamUtil to be installed:
https://github.com/statgen/bamUtil
"""
out_dir = os.path.dirname(pair[0])
if not out_prefix:
out_prefix = os.path.join(out_dir, "diff.bam")
else:
out_prefix = os.path.join(out_dir, out_prefix)
def get_out_file(out_prefix, in_file, number):
base, _ = os.path.splitext(out_prefix)
in_base, in_ext = os.path.splitext(os.path.basename(in_file))
out_file = "_".join([base, "only" + str(number), in_base]) + in_ext
return out_file
if not is_pair(pair):
raise ValueError("bamdiff needs to be run on a pair of input BAM "
"files.")
out_files = [get_out_file(out_prefix, y, x + 1)
for x, y in enumerate(pair)]
if all(map(file_exists, out_files)):
return out_files
sh.bam.diff("--in1", pair[0], "--in2", pair[1], "--out", out_prefix)
return out_files
def bamdiff(pair, out_prefix=None):
"""
takes two coordinate sorted BAM files and outputs only the records unique
to each one. requires bamUtil to be installed:
https://github.com/statgen/bamUtil
"""
out_dir = os.path.dirname(pair[0])
if not out_prefix:
out_prefix = os.path.join(out_dir, "diff.bam")
else:
out_prefix = os.path.join(out_dir, out_prefix)
def get_out_file(out_prefix, in_file, number):
base, _ = os.path.splitext(out_prefix)
in_base, in_ext = os.path.splitext(os.path.basename(in_file))
out_file = "_".join([base, "only" + str(number), in_base]) + in_ext
return out_file
if not is_pair(pair):
raise ValueError("bamdiff needs to be run on a pair of input BAM "
"files.")
out_files = [get_out_file(out_prefix, y, x + 1)
for x, y in enumerate(pair)]
if all(map(file_exists, out_files)):
return out_files
sh.bam.diff("--in1", pair[0], "--in2", pair[1], "--out", out_prefix)
return out_files
def __call__(self, in_file):
self._start_message(in_file)
if is_pair(in_file):
out_file = [run(x, self.stage_config, self.config) for x in in_file]
else:
out_file = run(in_file, self.stage_config, self.config)
self._end_message(in_file, out_file)
return out_file
def __call__(self, in_file):
self._start_message(in_file)
if is_pair(in_file):
out_file = [run(x, self.stage_config, self.config) for x in in_file]
else:
out_file = run(in_file, self.stage_config, self.config)
self._end_message(in_file, out_file)
return out_file
def __call__(self, in_file):
self._start_message(in_file)
if is_pair(in_file):
out_file = run_with_config(in_file[0], in_file[1],
self.ref, self.stage, self.config,
gtf=self.gtf)
else:
out_file = run_with_config(in_file[0], None, self.ref,
self.stage, self.config, gtf=self.gtf)
def __call__(self, in_file):
if is_pair(in_file):
out_files = self._run_pe(in_file)
return out_files
elif isinstance(in_file, str):
out_file = self._run_se(in_file)
return out_file
elif len(in_file) == 1:
out_file = self._run_se(in_file[0])
return out_file
else:
raise ValueError("Cutadapt can only run on either a single "
"file as a string or a pair of files to "
"handle paired end data.")
def __call__(self, in_file):
if is_pair(in_file):
out_files = self._run_pe(in_file)
return out_files
elif isinstance(in_file, str):
out_file = self._run_se(in_file)
return out_file
elif len(in_file) == 1:
out_file = self._run_se(in_file[0])
return out_file
else:
raise ValueError("Cutadapt can only run on either a single "
"file as a string or a pair of files to "
"handle paired end data.")
def __call__(self, in_file):
if isinstance(in_file, basestring):
logger.info("Detected %s as non-paired." % in_file)
out_file = run_with_config(in_file, None, self.ref,
self.stage, self.config)
elif is_pair(in_file):
logger.info("Detected %s as a pair." % in_file)
out_file = run_with_config(in_file[0], in_file[1],
self.ref, self.stage, self.config)
else:
logger.info("Detected %s as non-paired." % in_file)
out_file = run_with_config(in_file[0], None, self.ref,
self.stage, self.config)
return out_file
def __call__(self, in_file):
self._start_message(in_file)
out_file = self.out_file(in_file)
if file_exists(out_file):
return out_file
with file_transaction(out_file) as tmp_out_file:
if is_pair(in_file):
self._bowtie_pe(in_file, tmp_out_file)
else:
self._bowtie_se(in_file, tmp_out_file)
self._end_message(in_file)
return out_file
def __call__(self, in_file):
self._start_message(in_file)
out_file = self.out_file(in_file)
if file_exists(out_file):
return out_file
with file_transaction(out_file) as tmp_out_file:
if is_pair(in_file):
self._bowtie_pe(in_file, tmp_out_file)
else:
self._bowtie_se(in_file, tmp_out_file)
self._end_message(in_file)
return out_file
def out_file(self, in_file):
if is_pair(in_file):
return self._get_out_file(in_file[0])
else:
return self._get_out_file(in_file)
def out_file(self, in_file):
if is_pair(in_file):
return self._get_out_file(in_file[0])
else:
return self._get_out_file(in_file)
