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updated sorting
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@mwang87
mwang87 committed Mar 20, 2021
1 parent 8a0c7fa commit 79fd956
Showing 1 changed file with 27 additions and 23 deletions.
50 changes: 27 additions & 23 deletions shared_code/molecular_network_filtering_library.py
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Original file line number Diff line number Diff line change
Expand Up @@ -240,38 +240,42 @@ def add_clusterinfo_summary_to_graph(G, cluster_info_summary_filename):


def add_library_search_results_to_graph(G, library_search_filename, annotation_prefix=""):
row_count, table_data = ming_fileio_library.parse_table_with_headers(library_search_filename)
#row_count, table_data = ming_fileio_library.parse_table_with_headers(library_search_filename)
table_data_df = pd.read_csv(library_search_filename, sep='\t', dtype=str)

# sort in reverse match score order
try:
table_data = sorted(table_data, key=lambda x: float(x["MQScore"]), reverse=False)
table_data_df["MQScore"] = table_data_df["MQScore"].astype(float)
table_data_df = table_data_df.sort_values("MQScore", ascending=True)
except:
pass

row_count = len(table_data_df)
table_data = table_data_df.to_dict(orient="records")

for i in range(row_count):
cluster_index = table_data["#Scan#"][i]
for record in table_data:
cluster_index = str(record["#Scan#"])

if cluster_index in G.node:
G.node[cluster_index][annotation_prefix + "Adduct"] = str(table_data["Adduct"][i].encode('ascii', 'ignore'))
G.node[cluster_index][annotation_prefix + "Compound_Name"] = str(''.join([j if ord(j) < 128 else ' ' for j in table_data["Compound_Name"][i]]).replace("\\", "\\\\"))
G.node[cluster_index][annotation_prefix + "Adduct"] = str(table_data["Adduct"][i])
G.node[cluster_index][annotation_prefix + "INCHI"] = str(''.join([j if ord(j) < 128 else ' ' for j in table_data["INCHI"][i]]).replace("\\", "\\\\"))
G.node[cluster_index][annotation_prefix + "Smiles"] = str(''.join([j if ord(j) < 128 else ' ' for j in table_data["Smiles"][i]]).replace("\\", "\\\\"))
G.node[cluster_index][annotation_prefix + "MQScore"] = str(table_data["MQScore"][i])
G.node[cluster_index][annotation_prefix + "MassDiff"] = str(table_data["MassDiff"][i])
G.node[cluster_index][annotation_prefix + "MZErrorPPM"] = str(table_data["MZErrorPPM"][i])
G.node[cluster_index][annotation_prefix + "SharedPeaks"] = str(table_data["SharedPeaks"][i])
G.node[cluster_index][annotation_prefix + "tags"] = str(''.join([j if ord(j) < 128 else ' ' for j in table_data["tags"][i]]).replace("\\", "\\\\"))
G.node[cluster_index][annotation_prefix + "Library_Class"] = str(table_data["Library_Class"][i])
G.node[cluster_index][annotation_prefix + "Instrument"] = str(table_data["Instrument"][i])
G.node[cluster_index][annotation_prefix + "IonMode"] = str(table_data["IonMode"][i])
G.node[cluster_index][annotation_prefix + "Ion_Source"] = str(table_data["Ion_Source"][i])
G.node[cluster_index][annotation_prefix + "PI"] = str(table_data["PI"][i])
G.node[cluster_index][annotation_prefix + "Data_Collector"] = str(table_data["Data_Collector"][i])
G.node[cluster_index][annotation_prefix + "Compound_Source"] = str(table_data["Compound_Source"][i])
G.node[cluster_index][annotation_prefix + "SpectrumID"] = str(table_data["SpectrumID"][i])
G.node[cluster_index][annotation_prefix + "GNPSLibraryURL"] = "http://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=" + table_data["SpectrumID"][i]
G.node[cluster_index][annotation_prefix + "Adduct"] = str(record["Adduct"].encode('ascii', 'ignore'))
G.node[cluster_index][annotation_prefix + "Compound_Name"] = str(''.join([j if ord(j) < 128 else ' ' for j in record["Compound_Name"]]).replace("\\", "\\\\"))
G.node[cluster_index][annotation_prefix + "Adduct"] = str(record["Adduct"])
G.node[cluster_index][annotation_prefix + "INCHI"] = str(''.join([j if ord(j) < 128 else ' ' for j in str(record["INCHI"])]).replace("\\", "\\\\"))
G.node[cluster_index][annotation_prefix + "Smiles"] = str(''.join([j if ord(j) < 128 else ' ' for j in str(record["Smiles"])]).replace("\\", "\\\\"))
G.node[cluster_index][annotation_prefix + "MQScore"] = str(record["MQScore"])
G.node[cluster_index][annotation_prefix + "MassDiff"] = str(record["MassDiff"])
G.node[cluster_index][annotation_prefix + "MZErrorPPM"] = str(record["MZErrorPPM"])
G.node[cluster_index][annotation_prefix + "SharedPeaks"] = str(record["SharedPeaks"])
G.node[cluster_index][annotation_prefix + "tags"] = str(''.join([j if ord(j) < 128 else ' ' for j in str(record["tags"])]).replace("\\", "\\\\"))
G.node[cluster_index][annotation_prefix + "Library_Class"] = str(record["Library_Class"])
G.node[cluster_index][annotation_prefix + "Instrument"] = str(record["Instrument"])
G.node[cluster_index][annotation_prefix + "IonMode"] = str(record["IonMode"])
G.node[cluster_index][annotation_prefix + "Ion_Source"] = str(record["Ion_Source"])
G.node[cluster_index][annotation_prefix + "PI"] = str(record["PI"])
G.node[cluster_index][annotation_prefix + "Data_Collector"] = str(record["Data_Collector"])
G.node[cluster_index][annotation_prefix + "Compound_Source"] = str(record["Compound_Source"])
G.node[cluster_index][annotation_prefix + "SpectrumID"] = str(record["SpectrumID"])
G.node[cluster_index][annotation_prefix + "GNPSLibraryURL"] = "http://gnps.ucsd.edu/ProteoSAFe/gnpslibraryspectrum.jsp?SpectrumID=" + record["SpectrumID"]

try:
# ion identity networking specific:
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