def _adapterremoval_pe(config):
node_params = {"input_files_1" : ("tests/data/raw_reads/pe_reads_R1_001.fastq.gz",
"tests/data/raw_reads/pe_reads_R1_002.fastq.gz"),
"input_files_2" : ("tests/data/raw_reads/pe_reads_R2_001.fastq.gz",
"tests/data/raw_reads/pe_reads_R2_002.fastq.gz"),
"dependencies" : config.dependencies}
standard = PE_AdapterRemovalNode(output_prefix = os.path.join(config.destination, "pe_standard"),
**node_params)
custom = PE_AdapterRemovalNode.customize(output_prefix = os.path.join(config.destination, "pe_custom"),
**node_params)
custom.command.set_option("--minlength", 30)
return MetaNode(description = "AdapterRemoval_PE",
dependencies = [standard, custom.build_node()])
def _init_raw_reads(self, config, record):
version = VERSION_14
if record["Options"]["AdapterRemoval"]["Version"] == "v1.5+":
version = VERSION_15
output_format = record["Options"]["CompressionFormat"]
output_prefix = os.path.join(self.folder, "reads")
files = record["Data"]
if ("SE" in files):
# This returns a named tuple containing the parameters for the AdapterRemoval Node
command = SE_AdapterRemovalNode.customize(
input_files=files["SE"],
output_prefix=output_prefix,
output_format=output_format,
version=version)
self.files[
"Single"] = output_prefix + ".truncated." + output_format
else:
command = PE_AdapterRemovalNode.customize(
input_files_1=files["PE_1"],
input_files_2=files["PE_2"],
output_prefix=output_prefix,
output_format=output_format,
version=version)
self.files[
"Paired"] = output_prefix + ".pair{Pair}.truncated." + output_format
if version is VERSION_14:
self.files[
"Single"] = output_prefix + ".singleton.unaln.truncated." + output_format
self.files[
"Collapsed"] = output_prefix + ".singleton.aln.truncated." + output_format
else:
self.files[
"Single"] = output_prefix + ".singleton.truncated." + output_format
self.files[
"Collapsed"] = output_prefix + ".collapsed." + output_format
self.files[
"CollapsedTruncated"] = output_prefix + ".collapsed.truncated." + output_format
self.stats = output_prefix + ".settings"
quality_offset = self.quality_offset # record["Options"]["QualityOffset"]
if quality_offset == "Solexa":
quality_offset = 64
command.command.set_option("--qualitybase", quality_offset)
apply_options(command.command, record["Options"]["AdapterRemoval"])
self.nodes = (command.build_node(), )
def _init_raw_reads(self, record):
# Support for older versions of the pipeline, which used ARv1.0 - 1.4
version = VERSION_14
if record["Options"]["AdapterRemoval"]["Version"] == "v1.5+":
version = VERSION_15
quality_offset = self.quality_offset
if quality_offset == "Solexa":
quality_offset = 64
ar_options = dict(record["Options"]["AdapterRemoval"])
# Setup of "--collapsed" is handled by the node itself
collapse_reads = ar_options.pop("--collapse")
collapse_reads = collapse_reads or collapse_reads is None
init_args = {
"output_prefix": os.path.join(self.folder, "reads"),
"output_format": record["Options"]["CompressionFormat"],
"quality_offset": quality_offset,
"version": version
}
output_tmpl = "{output_prefix}.%s.{output_format}".format(**init_args)
if ("SE" in record["Data"]):
self.files["Single"] = output_tmpl % ("truncated", )
init_args["input_files"] = record["Data"]["SE"]
command = SE_AdapterRemovalNode.customize(**init_args)
else:
if version is VERSION_14:
self._set_adapterrm_v14_files(self.files, output_tmpl)
else:
self._set_adapterrm_v15_files(self.files, output_tmpl,
collapse_reads)
init_args["collapse"] = collapse_reads
init_args["input_files_1"] = record["Data"]["PE_1"]
init_args["input_files_2"] = record["Data"]["PE_2"]
command = PE_AdapterRemovalNode.customize(**init_args)
apply_options(command.command, ar_options)
self.stats = os.path.join(self.folder, "reads.settings")
self.nodes = (command.build_node(), )
def _init_raw_reads(self, config, record):
version = VERSION_14
if record["Options"]["AdapterRemoval"]["Version"] == "v1.5+":
version = VERSION_15
output_format = record["Options"]["CompressionFormat"]
output_prefix = os.path.join(self.folder, "reads")
files = record["Data"]
if ("SE" in files):
# This returns a named tuple containing the parameters for the AdapterRemoval Node
command = SE_AdapterRemovalNode.customize(input_files = files["SE"],
output_prefix = output_prefix,
output_format = output_format,
version = version)
self.files["Single"] = output_prefix + ".truncated." + output_format
else:
command = PE_AdapterRemovalNode.customize(input_files_1 = files["PE_1"],
input_files_2 = files["PE_2"],
output_prefix = output_prefix,
output_format = output_format,
version = version)
self.files["Paired"] = output_prefix + ".pair{Pair}.truncated." + output_format
if version is VERSION_14:
self.files["Single"] = output_prefix + ".singleton.unaln.truncated." + output_format
self.files["Collapsed"] = output_prefix + ".singleton.aln.truncated." + output_format
else:
self.files["Single"] = output_prefix + ".singleton.truncated." + output_format
self.files["Collapsed"] = output_prefix + ".collapsed." + output_format
self.files["CollapsedTruncated"] = output_prefix + ".collapsed.truncated." + output_format
self.stats = output_prefix + ".settings"
quality_offset = self.quality_offset # record["Options"]["QualityOffset"]
if quality_offset == "Solexa":
quality_offset = 64
command.command.set_option("--qualitybase", quality_offset)
apply_options(command.command, record["Options"]["AdapterRemoval"])
self.nodes = (command.build_node(),)
