def generate_rna_lib_profiling_results(configs_json: str, rna_items_json: str, output_file: str):
r"""
Generate RNA Lib "profiling" results file.
It should be called after "ShapeMapper 2.x" finishes the run.
Parameters
----------
configs_json: str
The "RNA Lib" configs, in `string` format
rna_items_json: str
The RNA Lib Item object
output_file: str
The "file path" of data output.
Returns
-------
"""
# Parse the "Python Object"
configs: RnaLibConfig = json.loads(configs_json, object_hook=as_python_object)
rna_items: List[LibraryItem] = json.loads(rna_items_json, object_hook=as_python_object)
#
updated_rna_items = []
for rna_item in rna_items:
#
rna_id = rna_item.rna_id
barcode = rna_item.barcode
# Load "Profile" data
shape_profile = get_shape2_path('profile', configs.working_folder, rna_id, barcode.barcode)
for nt_profile in io.parse(shape_profile, "shape-profile"):
#
nt_position = nt_profile.nt_position
rna_item.profile_list.append(nt_profile)
rna_item.profile_dict[nt_position] = nt_profile
# Load "Shape Reactivity" data
shape_reactivity = get_shape2_path('shape', configs.working_folder, rna_id, barcode.barcode)
for nt_reactivity in io.parse(shape_reactivity, "shape-reactivity"):
#
nt_position = nt_reactivity.nt_position
rna_item.shape_reactivity_list.append(nt_reactivity)
rna_item.shape_reactivity_dict[nt_position] = nt_reactivity
updated_rna_items.append(rna_item)
# Build RNA Library object
library = RnaLibrary()
library.load_meta(configs)
#
library.rna_items = updated_rna_items
# Output
data_str = json.dumps(library, cls=PythonObjectEncoder)
FileUtils.save_file(output_file, data_str)
def parse_bprna_annotation(structure_content: str) -> Tuple[str, SecondaryStructure]:
# use an intermediate tmp file because bpRNA needs it
out_tmp = open('tmp.dbn', 'w')
out_tmp.write(structure_content + '\n')
out_tmp.close()
#
subprocess.call(["bpRNA.pl", "tmp.dbn"], stdout=subprocess.PIPE)
#
in_tmp = open("tmp.st", 'r')
annotation = in_tmp.read()
in_tmp.close()
# Also parse the bpRNA contents
with open("tmp.st") as handle:
for secondary_structure in io.parse(handle, "bp-rna"):
#
return annotation, secondary_structure
def load(logger, config, bprna_folder_path, editing_level_file_path):
#
# Only load "bpRNA" file
bprna_files = [
f for f in os.listdir(bprna_folder_path)
if os.path.isfile(os.path.join(bprna_folder_path, f))
and os.path.splitext(f)[1] == '.st'
]
# bpRNA structures
bprna_structure_dict: Dict[str, SecondaryStructure] = dict()
for file in bprna_files:
#
file_path = os.path.join(bprna_folder_path, file)
with open(file_path) as handle:
for secondary_structure in io.parse(handle, "bp-rna"):
#
chromosome_id = secondary_structure.comment
bprna_structure_dict[chromosome_id] = secondary_structure
#
return bprna_files, bprna_structure_dict
# ----------------------------------
# region Pipeline - Prep
#
#
# The tool "PyPPL" cannot accept "python object" as input, we will need to convert it to
# "string" and then convert it back while using it.
# Load RNA Items
if not configs['rna_lib_file']:
raise ValueError('"RNA Lib" file load error. Please double check. ')
rna_lib_items = []
# A list of "RNA Lib items", each of which is in "python object string" format.
# It is used to pass via "Channel".
rna_lib_item_object_json_list = []
for rna_item in io.parse(configs['rna_lib_file'], "rna-lib-def"):
rna_lib_items.append(rna_item)
# Convert each item object to "json string"
rna_lib_item_object_json_list.append(
json.dumps(rna_item, cls=PythonObjectEncoder))
# Convert the objects to "string" and pass it as "argument"
configs_object_json = json.dumps(configs, cls=PythonObjectEncoder)
# A "python object string" format of a list, which includes a list of "RNA Lib items".
# It is used to passed as "whole"
rna_lib_items_list_json = json.dumps(rna_lib_items, cls=PythonObjectEncoder)
# endregion
# ----------------------------------
# region Pipeline - AfterQC
# ----------------------------------
# region Prep
if not os.path.isabs(output_file_path):
cwd = os.getcwd()
output_file_path = os.path.join(cwd, output_file_path)
# endregion
# ----------------------------------------------------------------
# region RNA Lib Items
#
rna_lib_items: List[LibraryItem] = []
for rna_item in io.parse(rna_lib_def_file_path, "rna-lib-def"):
rna_lib_items.append(rna_item)
# endregion
# ----------------------------------
# region QC
qc_results = []
#
os.chdir(dataset_folder_path)
# barcode = 'CGCGGTTGT'
# reverse = 'ACAACCGCG'
# cmd = 'cat {} | grep -E -c "^[ATCG]{{{}}}{}[ATCG]{{4}}{}"'.format(read_file_name, prefix, barcode, reverse)