def upload_alignment_set(self, alignment_items, alignmentset_name,
ws_name):
"""
Compiles and saves a set of alignment references (+ other stuff) into a
KBaseRNASeq.RNASeqAlignmentSet.
Returns the reference to the new alignment set.
alignment_items: [{
"ref": alignment_ref,
"label": condition label.
}]
# alignment_info = dict like this:
# {
# reads_ref: {
# "ref": alignment_ref
# }
# }
# reads_info = dict like this:
# {
# reads_ref: {
# "condition": "some condition"
# }
# }
# input_params = global input params to HISAT2, also has ws_name for the target workspace.
# alignmentset_name = name of final set object.
"""
print("Uploading completed alignment set")
alignment_set = {
"description":
"Alignments using HISAT2, v.{}".format(HISAT_VERSION),
"items": alignment_items
}
set_api = SetAPI(self.srv_wiz_url)
set_info = set_api.save_reads_alignment_set_v1({
"workspace": ws_name,
"output_object_name": alignmentset_name,
"data": alignment_set
})
return set_info["set_ref"]
class EditAlignmentSet:
"""
Constains a set of functions for expression levels calculations.
"""
PARAM_IN_WS_NAME_ID = 'workspace_name'
PARAM_IN_OBJ_NAME_ID = 'output_object_name'
PARAM_IN_ALIGNSET_REF = 'alignment_set_ref'
PARAM_IN_ALIGNS_ADD = 'alignments_to_add'
PARAM_IN_ALIGNS_RM = 'alignments_to_remove'
def __init__(self, config, logger=None):
self.config = config
self.logger = logger
self.callback_url = os.environ['SDK_CALLBACK_URL']
self.scratch = os.path.join(config['scratch'],
'EAS_' + str(uuid.uuid4()))
self.ws_url = config['workspace-url']
self.ws_client = Workspace(self.ws_url)
self.dfu = DataFileUtil(self.callback_url)
self.setAPI = SetAPI(self.callback_url)
pass
def _process_params(self, params):
"""
validates params passed to gen expression matrix method
"""
for p in [
self.PARAM_IN_ALIGNSET_REF, self.PARAM_IN_OBJ_NAME_ID,
self.PARAM_IN_WS_NAME_ID
]:
if p not in params:
raise ValueError(
'"{}" parameter is required, but missing'.format(p))
ws_name_id = params.get(self.PARAM_IN_WS_NAME_ID)
if not isinstance(ws_name_id, int):
try:
ws_name_id = self.dfu.ws_name_to_id(ws_name_id)
except DFUError as se:
prefix = se.message.split('.')[0]
raise ValueError(prefix)
alignments_to_add = params.get(self.PARAM_IN_ALIGNS_ADD)
alignments_to_remove = params.get(self.PARAM_IN_ALIGNS_RM)
if alignments_to_add is None and alignments_to_remove is None:
raise ValueError(
'Either "alignments_to_remove" or "alignments_to_add" should be given'
)
return ws_name_id
def _get_type_from_obj_info(self, info):
return info[2].split('-')[0]
def _get_obj_info(self, ref):
return self.ws_client.get_object_info3({'objects': [{
'ref': ref
}]})['infos'][0]
def _get_set_items(self, alignment_set_ref):
obj_info = self._get_obj_info(alignment_set_ref)
obj_type = self._get_type_from_obj_info(obj_info)
if obj_type in ['KBaseSets.ReadsAlignmentSet']:
set_data = self.setAPI.get_reads_alignment_set_v1(
{'ref': alignment_set_ref})
items = set_data['data']['items']
elif obj_type in ['KBaseRNASeq.RNASeqAlignmentSet']:
alignmentset_obj = self.ws_client.get_objects2(
{'objects': [{
'ref': alignment_set_ref
}]})['data'][0]
"""
Add each alignment object to align_item and add it to items list
"""
items = list()
for alignment_ref in alignmentset_obj['data']['sample_alignments']:
align_item = dict()
align_item['ref'] = alignment_ref
items.append(align_item)
else:
raise ValueError(
'"alignment_set_ref" should be of type KBaseSets.ReadsAlignmentSet or '
+ 'KBaseRNASeq.RNASeqAlignmentSet')
return items
def _add_alignments(self, alignment_set_items, alignment_refs_list):
for alignment_ref in alignment_refs_list:
found = False
for set_item in alignment_set_items:
if set_item.get('ref') == alignment_ref:
print('{} already in the input Alignment Set. Not added'.
format(alignment_ref))
found = True
break
if not found:
alignment_set_items.append({'ref': alignment_ref})
return alignment_set_items
def _remove_alignments(self, input_alignment_set, alignment_set_items,
alignments_to_remove):
for input_item in input_alignment_set:
if not (input_item.get('ref') in alignments_to_remove):
alignment_set_items.append(input_item)
return alignment_set_items
def _save_alignment_set(self, ws_name, obj_name, set_data):
res = self.setAPI.save_reads_alignment_set_v1({
"workspace": ws_name,
"output_object_name": obj_name,
"data": set_data
})
return res.get('set_ref')
def edit_alignment_set(self, params):
ws_name_id = self._process_params(params)
obj_name = params.get(self.PARAM_IN_OBJ_NAME_ID)
alignment_set_ref = params.get(self.PARAM_IN_ALIGNSET_REF)
print('INPUT ALIGNMENT SET REF: ' + alignment_set_ref)
input_alignment_set = self._get_set_items(alignment_set_ref)
alignments_to_remove = params.get(self.PARAM_IN_ALIGNS_RM, None)
alignments_to_add = params.get(self.PARAM_IN_ALIGNS_ADD, None)
set_items = list()
if alignments_to_remove is not None:
set_items = self._remove_alignments(input_alignment_set, set_items,
alignments_to_remove)
if alignments_to_add is not None:
set_items = self._add_alignments(set_items, alignments_to_add)
set_data = {
'description': 'Edited from {}'.format(alignment_set_ref),
'items': set_items
}
output_alignment_set_ref = self._save_alignment_set(
ws_name_id, obj_name, set_data)
return output_alignment_set_ref