def create_run_spec_given_datasources(input_format, output_format, input_filename, output_filename, global_annotations=None,
datasource_list=None, genomeBuild="hg19", is_multicore=False, num_cores=4,
default_annotations=None, cache_url=None, read_only_cache=True,
tx_mode=TranscriptProvider.TX_MODE_CANONICAL, is_skip_no_alts=False, other_opts=None, annotating_type=None):
"""Same as create_run_spec, but a list of datasource instances can be used. Typically, this method is only called
by automated tests."""
global_annotations = dict() if global_annotations is None else global_annotations
default_annotations = dict() if default_annotations is None else default_annotations
datasource_list = [] if datasource_list is None else datasource_list
other_opts = dict() if other_opts is None else other_opts
if input_format == "TCGAMAF" and not other_opts.get(OptionConstants.REANNOTATE_TCGA_MAF_COLS, False):
other_opts[OptionConstants.REANNOTATE_TCGA_MAF_COLS] = True
other_opts[InputMutationCreatorOptions.IS_SKIP_ALTS] = is_skip_no_alts
# Step 0 Validate given parameters and log messages. If an error or critical is found, throw an exception.
validation_messages = RunSpecificationFactory._validate_run_spec_parameters(input_format, output_format, input_filename, output_filename, global_annotations,
datasource_list, genomeBuild, is_multicore, num_cores,
default_annotations, cache_url, read_only_cache,
tx_mode, is_skip_no_alts, other_opts, annotating_type)
for msg in validation_messages:
logging.getLogger(__name__).log(msg.level, msg.message)
if (msg.level == logging.ERROR) or (msg.level == logging.CRITICAL):
raise RunSpecificationException(msg.message)
# Step 1 Initialize input and output
is_allow_annotation_overwriting = other_opts.get(OptionConstants.ALLOW_ANNOTATION_OVERWRITING, False)
mutation_data_factory = MutationDataFactory(is_allow_annotation_overwriting)
inputCreator = OncotatorCLIUtils.create_input_creator(input_filename, input_format, mutation_data_factory, genomeBuild, other_opts)
outputRenderer = OncotatorCLIUtils.create_output_renderer(output_filename, output_format, other_opts)
result = RunSpecification()
result.initialize(inputCreator, outputRenderer, manualAnnotations=global_annotations, datasources=datasource_list,
isMulticore=is_multicore, numCores=num_cores, defaultAnnotations=default_annotations,
cacheUrl=cache_url, read_only_cache=read_only_cache, is_skip_no_alts=is_skip_no_alts, annotating_type=annotating_type,
is_allow_annotation_overwriting=is_allow_annotation_overwriting)
return result
def create_run_spec_given_datasources(input_format, output_format, input_filename, output_filename, global_annotations=None,
datasource_list=None, genomeBuild="hg19", is_multicore=False, num_cores=4,
default_annotations=None, cache_url=None, read_only_cache=True,
tx_mode=TranscriptProvider.TX_MODE_CANONICAL, is_skip_no_alts=False, other_opts=None, annotating_type=None):
"""Same as create_run_spec, but a list of datasource instances can be used. Typically, this method is only called
by automated tests."""
global_annotations = dict() if global_annotations is None else global_annotations
default_annotations = dict() if default_annotations is None else default_annotations
datasource_list = [] if datasource_list is None else datasource_list
other_opts = dict() if other_opts is None else other_opts
if input_format == "TCGAMAF" and not other_opts.get(OptionConstants.REANNOTATE_TCGA_MAF_COLS, False):
other_opts[OptionConstants.REANNOTATE_TCGA_MAF_COLS] = True
other_opts[InputMutationCreatorOptions.IS_SKIP_ALTS] = is_skip_no_alts
# Step 0 Validate given parameters and log messages. If an error or critical is found, throw an exception.
validation_messages = RunSpecificationFactory._validate_run_spec_parameters(input_format, output_format, input_filename, output_filename, global_annotations,
datasource_list, genomeBuild, is_multicore, num_cores,
default_annotations, cache_url, read_only_cache,
tx_mode, is_skip_no_alts, other_opts, annotating_type)
for msg in validation_messages:
logging.getLogger(__name__).log(msg.level, msg.message)
if (msg.level == logging.ERROR) or (msg.level == logging.CRITICAL):
raise RunSpecificationException(msg.message)
# Step 1 Initialize input and output
is_allow_annotation_overwriting = other_opts.get(OptionConstants.ALLOW_ANNOTATION_OVERWRITING, False)
mutation_data_factory = MutationDataFactory(is_allow_annotation_overwriting)
inputCreator = OncotatorCLIUtils.create_input_creator(input_filename, input_format, mutation_data_factory, genomeBuild, other_opts)
outputRenderer = OncotatorCLIUtils.create_output_renderer(output_filename, output_format, other_opts)
result = RunSpecification()
result.initialize(inputCreator, outputRenderer, manualAnnotations=global_annotations, datasources=datasource_list,
isMulticore=is_multicore, numCores=num_cores, defaultAnnotations=default_annotations,
cacheUrl=cache_url, read_only_cache=read_only_cache, is_skip_no_alts=is_skip_no_alts, annotating_type=annotating_type,
is_allow_annotation_overwriting=is_allow_annotation_overwriting)
return result
def create_run_spec(
inputFormat,
outputFormat,
inputFilename,
outputFilename,
globalAnnotations=None,
datasourceDir=None,
genomeBuild="hg19",
isMulticore=False,
numCores=4,
defaultAnnotations=None,
cacheUrl=None,
read_only_cache=True,
tx_mode=TranscriptProvider.TX_MODE_CANONICAL,
is_skip_no_alts=False,
other_opts=None,
annotating_type=None,
):
""" This is a very simple interface to start an Oncotator session. As a warning, this interface may notbe supported in future versions.
If datasourceDir is None, then the default location is used. TODO: Define default location.
IMPORTANT: Current implementation attempts to annotate using a default set of datasources.
TODO: Make sure that this note above is no longer the case. Current implementation attempts to annotate using a default set of datasources
TODO: This method may get refactored into a separate class that handles RunConfigutaion objects.
"""
# TODO: Use dependency injection for list of name value pairs? Otherwise, set it up as an attribute on this class.
# TODO: Use dependency injection to return instance of the input/output classes
globalAnnotations = dict() if globalAnnotations is None else globalAnnotations
defaultAnnotations = dict() if defaultAnnotations is None else defaultAnnotations
other_opts = dict() if other_opts is None else other_opts
other_opts[InputMutationCreatorOptions.IS_SKIP_ALTS] = is_skip_no_alts
# Step 0 Validate given parameters and log messages. If an error or critical is found, throw an exception.
validation_messages = RunSpecificationFactory._validate_run_spec_parameters(
inputFormat,
outputFormat,
inputFilename,
outputFilename,
globalAnnotations,
datasourceDir,
genomeBuild,
isMulticore,
numCores,
defaultAnnotations,
cacheUrl,
read_only_cache,
tx_mode,
is_skip_no_alts,
other_opts,
annotating_type,
)
for msg in validation_messages:
logging.getLogger(__name__).log(msg.level, msg.message)
if (msg.level == logging.ERROR) or (msg.level == logging.CRITICAL):
raise RunSpecificationException(msg.message)
# Step 1 Initialize input and output
inputCreator = OncotatorCLIUtils.create_input_creator(inputFilename, inputFormat, genomeBuild, other_opts)
outputRenderer = OncotatorCLIUtils.create_output_renderer(outputFilename, outputFormat, other_opts)
# Step 2 Datasources
datasource_list = DatasourceFactory.createDatasources(
datasourceDir, genomeBuild, isMulticore=isMulticore, numCores=numCores, tx_mode=tx_mode
)
# TODO: Refactoring needed here to specify tx-mode (or any option not in a config file) in a cleaner way.
for ds in datasource_list:
if isinstance(ds, TranscriptProvider):
logging.getLogger(__name__).info("Setting %s %s to tx-mode of %s..." % (ds.title, ds.version, tx_mode))
ds.set_tx_mode(tx_mode)
result = RunSpecification()
result.initialize(
inputCreator,
outputRenderer,
manualAnnotations=globalAnnotations,
datasources=datasource_list,
isMulticore=isMulticore,
numCores=numCores,
defaultAnnotations=defaultAnnotations,
cacheUrl=cacheUrl,
read_only_cache=read_only_cache,
is_skip_no_alts=is_skip_no_alts,
annotating_type=annotating_type,
)
return result
def create_run_spec(inputFormat,
outputFormat,
inputFilename,
outputFilename,
globalAnnotations=None,
datasourceDir=None,
genomeBuild="hg19",
isMulticore=False,
numCores=4,
defaultAnnotations=None,
cacheUrl=None,
read_only_cache=True,
tx_mode=TranscriptProvider.TX_MODE_CANONICAL,
is_skip_no_alts=False,
other_opts=None,
annotating_type=None):
""" This is a very simple interface to start an Oncotator session. As a warning, this interface may notbe supported in future versions.
If datasourceDir is None, then the default location is used. TODO: Define default location.
IMPORTANT: Current implementation attempts to annotate using a default set of datasources.
TODO: Make sure that this note above is no longer the case. Current implementation attempts to annotate using a default set of datasources
TODO: This method may get refactored into a separate class that handles RunConfigutaion objects.
"""
# TODO: Use dependency injection for list of name value pairs? Otherwise, set it up as an attribute on this class.
# TODO: Use dependency injection to return instance of the input/output classes
globalAnnotations = dict(
) if globalAnnotations is None else globalAnnotations
defaultAnnotations = dict(
) if defaultAnnotations is None else defaultAnnotations
other_opts = dict() if other_opts is None else other_opts
other_opts[InputMutationCreatorOptions.IS_SKIP_ALTS] = is_skip_no_alts
# Step 0 Validate given parameters and log messages. If an error or critical is found, throw an exception.
validation_messages = RunSpecificationFactory._validate_run_spec_parameters(
inputFormat, outputFormat, inputFilename, outputFilename,
globalAnnotations, datasourceDir, genomeBuild, isMulticore,
numCores, defaultAnnotations, cacheUrl, read_only_cache, tx_mode,
is_skip_no_alts, other_opts, annotating_type)
for msg in validation_messages:
logging.getLogger(__name__).log(msg.level, msg.message)
if (msg.level == logging.ERROR) or (msg.level == logging.CRITICAL):
raise RunSpecificationException(msg.message)
# Step 1 Initialize input and output
inputCreator = OncotatorCLIUtils.create_input_creator(
inputFilename, inputFormat, genomeBuild, other_opts)
outputRenderer = OncotatorCLIUtils.create_output_renderer(
outputFilename, outputFormat, other_opts)
# Step 2 Datasources
if datasourceDir:
datasource_list = DatasourceFactory.createDatasources(
datasourceDir,
genomeBuild,
isMulticore=isMulticore,
numCores=numCores,
tx_mode=tx_mode)
else:
datasource_list = []
#TODO: Refactoring needed here to specify tx-mode (or any option not in a config file) in a cleaner way.
for ds in datasource_list:
if isinstance(ds, TranscriptProvider):
logging.getLogger(__name__).info(
"Setting %s %s to tx-mode of %s..." %
(ds.title, ds.version, tx_mode))
ds.set_tx_mode(tx_mode)
if other_opts.get(
OptionConstants.CUSTOM_CANONICAL_TX_LIST_FILE,
None) is not None:
cc_txs_fp = file(
other_opts[
OptionConstants.CUSTOM_CANONICAL_TX_LIST_FILE],
'r')
cc_txs = [tx.rsplit(".", 1)[0] for tx in cc_txs_fp]
cc_txs_fp.close()
ds.set_custom_canonical_txs(cc_txs)
logging.getLogger(__name__).info(
str(len(cc_txs)) +
" custom canonical transcripts specified.")
else:
logging.getLogger(__name__).info(
"No custom canonical transcripts specified.")
result = RunSpecification()
result.initialize(inputCreator,
outputRenderer,
manualAnnotations=globalAnnotations,
datasources=datasource_list,
isMulticore=isMulticore,
numCores=numCores,
defaultAnnotations=defaultAnnotations,
cacheUrl=cacheUrl,
read_only_cache=read_only_cache,
is_skip_no_alts=is_skip_no_alts,
annotating_type=annotating_type)
return result