def __init__(self, config, target_name, input_files, output_file,
regions_file=None, dependencies=()):
bam_input = MultiBAMInput(config, input_files)
if len(bam_input.files) > 1 and regions_file:
raise ValueError("DepthHistogram for regions require single, "
"indexed input BAM file.")
builder = factory.new("depths")
builder.add_value("%(TEMP_IN_BAM)s")
builder.add_value("%(OUT_FILE)s")
builder.set_option("--target-name", target_name)
builder.set_kwargs(OUT_FILE=output_file)
bam_input.setup(builder)
if regions_file:
builder.set_option('--regions-file', '%(IN_REGIONS)s')
builder.set_kwargs(IN_REGIONS=regions_file)
command = ParallelCmds(bam_input.commands + [builder.finalize()])
description = "<DepthHistogram: %s -> '%s'>" \
% (describe_files(bam_input.files), output_file)
MultiBAMInputNode.__init__(self,
bam_input=bam_input,
command=command,
description=description,
dependencies=dependencies)
def __init__(self, parameters):
bam_input = MultiBAMInput(parameters.config, parameters.input_files)
bam_input.setup(parameters.command)
cmd_map = parameters.command.finalize()
description = "<mapDamage (plots): %s -> '%s'>" \
% (describe_files(parameters.input_files),
parameters.output_directory)
MultiBAMInputNode.__init__(self,
bam_input=bam_input,
command=ParallelCmds(bam_input.commands +
[cmd_map]),
description=description,
dependencies=parameters.dependencies)
def __init__(self, parameters):
bam_input = MultiBAMInput(parameters.config, parameters.input_files)
bam_input.setup(parameters.command)
cmd_map = parameters.command.finalize()
description = "<mapDamage (plots): %s -> '%s'>" \
% (describe_files(parameters.input_files),
parameters.output_directory)
MultiBAMInputNode.__init__(self,
bam_input=bam_input,
command=ParallelCmds(bam_input.commands +
[cmd_map]),
description=description,
dependencies=parameters.dependencies)
def __init__(self, config, input_files, output_file, dependencies=()):
bam_input = MultiBAMInput(config, input_files)
duphist_command = factory.new("duphist")
duphist_command.add_value("%(TEMP_IN_BAM)s")
duphist_command.set_kwargs(OUT_STDOUT=output_file)
bam_input.setup(duphist_command)
duphist_command = duphist_command.finalize()
commands = ParallelCmds(bam_input.commands + [duphist_command])
description = "<DuplicateHistogram: %s -> %r>" % (describe_files(input_files), output_file)
MultiBAMInputNode.__init__(
self, bam_input=bam_input, command=commands, description=description, dependencies=dependencies
)
def __init__(self, parameters):
self._directory = parameters.directory
bam_input = MultiBAMInput(parameters.config, parameters.input_files)
bam_input.setup(parameters.command)
command = parameters.command.finalize()
description = "<mapDamage (rescale): %s -> %r>" \
% (describe_files(parameters.input_files),
parameters.output_file)
MultiBAMInputNode.__init__(self,
bam_input=bam_input,
command=ParallelCmds(bam_input.commands +
[command]),
description=description,
dependencies=parameters.dependencies)
def __init__(self, parameters):
self._directory = parameters.directory
bam_input = MultiBAMInput(parameters.config, parameters.input_files)
bam_input.setup(parameters.command)
command = parameters.command.finalize()
description = "<mapDamage (rescale): %s -> %r>" \
% (describe_files(parameters.input_files),
parameters.output_file)
MultiBAMInputNode.__init__(self,
bam_input=bam_input,
command=ParallelCmds(bam_input.commands +
[command]),
description=description,
dependencies=parameters.dependencies)
def __init__(self, config, input_bams, output_bam, keep_dupes=True, dependencies=()):
bam_input = MultiBAMInput(config, input_bams)
builder = factory.new("rmdup_collapsed")
builder.add_value("%(TEMP_IN_BAM)s")
builder.set_kwargs(OUT_STDOUT=output_bam)
bam_input.setup(builder)
if not keep_dupes:
builder.set_option("--remove-duplicates")
filteruniq = builder.finalize()
command = ParallelCmds(bam_input.commands + [filteruniq])
description = "<FilterCollapsedBAM: %s>" % (describe_files(bam_input.files),)
MultiBAMInputNode.__init__(
self, bam_input=bam_input, command=command, description=description, dependencies=dependencies
)
def __init__(self, config, input_files, output_file, dependencies=()):
bam_input = MultiBAMInput(config, input_files)
duphist_command = factory.new("duphist")
duphist_command.add_value('%(TEMP_IN_BAM)s')
duphist_command.set_kwargs(OUT_STDOUT=output_file)
bam_input.setup(duphist_command)
duphist_command = duphist_command.finalize()
commands = ParallelCmds(bam_input.commands + [duphist_command])
description = "<DuplicateHistogram: %s -> %r>" \
% (describe_files(input_files), output_file)
MultiBAMInputNode.__init__(self,
bam_input=bam_input,
command=commands,
description=description,
dependencies=dependencies)
def __init__(self, config, target_name, input_files, output_file, regions_file=None, dependencies=()):
bam_input = MultiBAMInput(config, input_files)
if len(bam_input.files) > 1 and regions_file:
raise ValueError("DepthHistogram for regions require single, " "indexed input BAM file.")
builder = factory.new("depths")
builder.add_value("%(TEMP_IN_BAM)s")
builder.add_value("%(OUT_FILE)s")
builder.set_option("--target-name", target_name)
builder.set_kwargs(OUT_FILE=output_file)
bam_input.setup(builder)
if regions_file:
builder.set_option("--regions-file", "%(IN_REGIONS)s")
builder.set_kwargs(IN_REGIONS=regions_file)
command = ParallelCmds(bam_input.commands + [builder.finalize()])
description = "<DepthHistogram: %s -> '%s'>" % (describe_files(bam_input.files), output_file)
MultiBAMInputNode.__init__(
self, bam_input=bam_input, command=command, description=description, dependencies=dependencies
)
def __init__(self, config, input_bams, output_bam, keep_dupes=True,
dependencies=()):
bam_input = MultiBAMInput(config, input_bams)
builder = factory.new("rmdup_collapsed")
builder.add_value("%(TEMP_IN_BAM)s")
builder.set_kwargs(OUT_STDOUT=output_bam)
bam_input.setup(builder)
if not keep_dupes:
builder.set_option("--remove-duplicates")
filteruniq = builder.finalize()
command = ParallelCmds(bam_input.commands + [filteruniq])
description = "<FilterCollapsedBAM: %s>" \
% (describe_files(bam_input.files),)
MultiBAMInputNode.__init__(self,
bam_input=bam_input,
command=command,
description=description,
dependencies=dependencies)