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
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 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