def upload_STARalignment(self, input_params, reads_ref, reads_info, output_bam_file):
"""
Uploads the alignment file + metadata.
Returns the STAR alignment reference.
"""
aligner_opts = dict()
for k in input_params:
aligner_opts[k] = str(input_params[k])
pprint(reads_info)
alignment_name = reads_ref['alignment_output_name']
align_upload_params = {
"destination_ref": "{}/{}".format(input_params[self.PARAM_IN_WS], alignment_name),
"file_path": output_bam_file,
"assembly_or_genome_ref": input_params[self.PARAM_IN_GENOME],
"read_library_ref": reads_info['object_ref'],
"library_type": reads_info['style'],
"condition": reads_info['condition'],
"aligned_using": 'STAR',
"aligner_version":self.STAR_VERSION,
"aligner_opts": aligner_opts
}
pprint(align_upload_params)
ra_util = ReadsAlignmentUtils(self.callback_url, service_ver='beta')
rau_upload_ret = ra_util.upload_alignment(align_upload_params)
alignment_ref = rau_upload_ret["obj_ref"]
print("STAR alignment uploaded as object {}".format(alignment_ref))
return rau_upload_ret
def save_read_alignment_output(self, run_output_info, input_configuration, validated_params):
rau = ReadsAlignmentUtils(self.callback_url)
destination_ref = validated_params['output_workspace'] + '/' + validated_params['output_alignment_name']
condition = 'unknown'
if 'condition_label' in validated_params:
condition = validated_params['condition_label']
upload_params = {'file_path': run_output_info['output_sam_file'],
'destination_ref': destination_ref,
'read_library_ref': input_configuration['reads_lib_ref'],
'assembly_or_genome_ref': validated_params['assembly_or_genome_ref'],
'condition': condition}
upload_results = rau.upload_alignment(upload_params)
return upload_results
def load_bam_file(self, file_path, genome_ref, reads_ref, obj_name):
rau = ReadsAlignmentUtils(self.callback_url, service_ver='dev')
return rau.upload_alignment({
"destination_ref":
"{}/{}".format(self.ws_name, obj_name),
"file_path":
file_path,
"read_library_ref":
reads_ref,
"assembly_or_genome_ref":
genome_ref,
"condition":
"none"
})["obj_ref"]
def upload_alignment(self, input_params, reads_info, alignment_name,
alignment_file):
"""
Uploads the alignment file + metadata.
This then returns the expected return dictionary from HISAT2.
"""
aligner_opts = dict()
for k in input_params:
aligner_opts[k] = str(input_params[k])
align_upload_params = {
"destination_ref":
"{}/{}".format(input_params["ws_name"], alignment_name),
"file_path":
alignment_file,
"library_type":
reads_info["style"], # single or paired end,
"condition":
reads_info["condition"],
"assembly_or_genome_ref":
input_params["genome_ref"],
"read_library_ref":
reads_info["object_ref"],
"aligned_using":
"hisat2",
"aligner_version":
HISAT_VERSION,
"aligner_opts":
aligner_opts
}
if "sampleset_ref" in reads_info:
align_upload_params["sampleset_ref"] = reads_info["sampleset_ref"]
print("Uploading completed alignment")
pprint(align_upload_params)
ra_util = ReadsAlignmentUtils(self.callback_url, service_ver="dev")
alignment_ref = ra_util.upload_alignment(
align_upload_params)["obj_ref"]
print(
"Done! New alignment uploaded as object {}".format(alignment_ref))
return alignment_ref
def upload_alignment(self, file_path, reads_upa, assembly_upa, workspace_name, alignment_name):
if not file_path:
raise ValueError("file_path must be defined")
if not os.path.exists(file_path):
raise ValueError("The given alignment file '{}' does not exist".format(file_path))
if not reads_upa:
raise ValueError("The reads UPA must be defined")
if not assembly_upa:
raise ValueError("The assembly UPA must be defined")
if not workspace_name:
raise ValueError("workspace_name must be defined")
if not alignment_name:
raise ValueError("alignment_name must be defined")
rau = ReadsAlignmentUtils(self.callback_url)
alignment_upa = rau.upload_alignment({
"file_path": file_path,
"read_library_ref": reads_upa,
"assembly_or_genome_ref": assembly_upa,
"destination_ref": "{}/{}".format(workspace_name, alignment_name),
"aligned_using": "BBMap",
"condition": "new_assembly"
})["obj_ref"]
return alignment_upa