def onstart(**k):
#_gnps_list = utils.load_GNPS(library_names=["GNPS-LIBRARY"])
_gnps_list = utils.load_GNPS()
_gnps_list = utils.gnps_format_libraries(_gnps_list)
gnps_df = pd.DataFrame(_gnps_list)
gnps_df.to_feather("gnps_list.feather")
def test_filtered_spectra():
import utils
spectra_list = utils.load_GNPS(library_names=["GNPS-LIBRARY"])
spectra_list = utils.gnps_format_libraries(spectra_list)
with open("output_enriched_list.json", "w") as output_file:
output_file.write(json.dumps(spectra_list, indent=4))
filtered_list = utils.gnps_filter_for_key(spectra_list)
with open("output_filtered_list.json", "w") as output_file:
output_file.write(json.dumps(filtered_list, indent=4))
print(len(filtered_list))
def generate_gnps_data():
# Loading all GNPS Library Spectra, without peaks
gnps_libraries = utils.load_GNPS()
print("Got all Libraries")
with open("/output/gnpslibraries.json", "w") as output_file:
output_file.write(json.dumps(gnps_libraries))
encriched_gnps_libraries = utils.gnps_format_libraries(gnps_libraries)
print("Enriched Libraries")
with open("/output/gnpslibraries_enriched_all.json", "w") as output_file:
output_file.write(
json.dumps(
utils.gnps_filter_for_key(encriched_gnps_libraries,
filterKeysOut=False)))
#Outputting for NPAtlas
with open("/output/gnpslibraries_npatlas.json", "w") as output_file:
output_file.write(
json.dumps(
utils.gnps_filter_for_key(encriched_gnps_libraries,
filterKeysOut=True)))
pd.DataFrame(utils.gnps_filter_for_key(encriched_gnps_libraries)).to_csv(
"/output/gnpslibraries_npatlas.tsv", sep="\t", index=False)
print("NPAtlas Export")
# Getting spectrum peaks for each library spectrum
print("Individual Library Export")
encriched_gnps_libraries_with_peaks = utils.output_all_gnps_individual_libraries(
encriched_gnps_libraries, "/output/")
with open("/output/ALL_GNPS.json", "w") as output_file:
output_file.write(json.dumps(encriched_gnps_libraries_with_peaks))
print("MGF Library Export")
# Generating the MGF versions of it
mgf_string = utils.get_full_mgf_string(encriched_gnps_libraries_with_peaks)
with open("/output/ALL_GNPS.mgf", "wb") as output_file:
output_file.write(mgf_string.encode("ascii", "ignore"))
print("MSP Library Export")
# TODO: Generating the MSP versions of it
msp_string = utils.get_full_msp_string(encriched_gnps_libraries_with_peaks)
with open("/output/ALL_GNPS.msp", "wb") as output_file:
output_file.write(msp_string.encode("ascii", "ignore"))
def test_get_library_peaks_full():
import utils
output_folder = "."
spectra_list = utils.load_GNPS()
spectra_list = utils.gnps_format_libraries(spectra_list)
spectra_list_with_peaks = utils.output_all_gnps_individual_libraries(
spectra_list, ".")
with open("ALL_GNPS.json", "w") as output_file:
output_file.write(json.dumps(spectra_list_with_peaks, indent=4))
mgf_string = utils.get_full_mgf_string(spectra_list_with_peaks)
with open("ALL_GNPS.mgf", "wb") as output_file:
output_file.write(mgf_string.encode("ascii", "ignore"))
msp_string = utils.get_full_msp_string(spectra_list_with_peaks)
with open("ALL_GNPS.msp", "wb") as output_file:
output_file.write(msp_string.encode("ascii", "ignore"))
def test_get_library_peaks():
import utils
spectra_list = utils.load_GNPS(library_names=["GNPS-LIBRARY"])[:100]
spectra_list = utils.gnps_format_libraries(spectra_list)
spectra_list_with_peaks = utils.output_all_gnps_individual_libraries(
spectra_list, ".")
print(len(spectra_list_with_peaks))
with open("ALL_GNPS.json", "w") as output_file:
output_file.write(json.dumps(spectra_list_with_peaks, indent=4))
mgf_string = utils.get_full_mgf_string(spectra_list_with_peaks)
with open("ALL_GNPS.mgf", "wb") as output_file:
output_file.write(mgf_string.encode("ascii", "ignore"))
msp_string = utils.get_full_msp_string(spectra_list_with_peaks)
with open("ALL_GNPS.msp", "wb") as output_file:
output_file.write(msp_string.encode("ascii", "ignore"))
library_name = "ALL_GNPS"
library_dict = {}
library_dict["libraryname"] = library_name
library_dict["mgflink"] = "/gnpslibrary/{}.mgf".format(library_name)
library_dict["msplink"] = "/gnpslibrary/{}.msp".format(library_name)
library_dict["jsonlink"] = "/gnpslibrary/{}.json".format(library_name)
library_list.append(library_dict)
return render_template('gnpslibrarylist.html', library_list=library_list)
@app.route('/gnpslibrary/<library>.mgf', methods=['GET'])
def mgf_download(library):
return send_from_directory("/output", "{}.mgf".format(library))
@app.route('/gnpslibrary/<library>.msp', methods=['GET'])
def msp_download(library):
return send_from_directory("/output", "{}.msp".format(library))
@app.route('/gnpslibrary/<library>.json', methods=['GET'])
def json_download(library):
return send_from_directory("/output", "{}.json".format(library))
npatlas_list = utils.load_NPAtlas("data/npatlas.json")
mibig_list = utils.load_mibig("data/mibig.csv")
gnps_list = utils.load_GNPS()
gnps_list = utils.gnps_format_libraries(gnps_list)