Data parsing function

data_parsing_function.py

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+def merge(names,nodes,delnodes,merged):
+
+    #import librarys.
+    import csv  
+    import pandas as pd
+
+    #create empty DataFrame df_names and df_nodes.
+    df_names = pd.DataFrame()
+    df_nodes = pd.DataFrame()
+
+    #read .dmp files with use of parameters.
+    df_names = pd.read_csv(names,delimiter='\t',header=None)
+    df_nodes = pd.read_csv(nodes,delimiter='\t',header=None)
+
+    #collect usefull columns from DataFrames.
+    df_nodes = df_nodes[[0,2,4]] 
+    df_names = df_names[[0, 2, 6]]
+
+    #apply key on column 6 in df_named and extract column 0 and 2.
+    df_names = df_names[df_names[6]=='scientific name'][[0,2]]
+
+    #lenth of dataframe in range(.....).
+    df_names.index = range(len(df_names))
+
+    #merge both DataFrames df_nodes and df_names in new DataFrame df_merge.
+    df_merge = pd.DataFrame()
+    df_merge = df_nodes.merge(df_names[[0,2]],how = "left",left_on = [0],right_on= [0])
+
+    #rename columns of DataFrame df_merge.
+    df_merge = df_merge.rename(columns={0:'taxa_ids','2_x':'parent_id',4:'rank','2_y':'scientfic_name'})
+
+    #create empty DataFrame df_delnodes and df_merged.
+    df_delnodes = pd.DataFrame()
+    df_merged = pd.DataFrame()
+    #read .dmp files with use of parameters.
+    df_delnodes = pd.read_csv(delnodes,delimiter='\t',header=None)
+    df_merged = pd.read_csv(merged,delimiter='\t',header=None)
+
+    #creat two empty lists taxaid and taxaids assign them with set of df_merge['taxa_ids'] and df_merged[0].
+    taxaid = list(set(df_merge['taxa_ids']))
+    taxaids = list(set(df_merged[0]))
+
+    #print common values in lists.
+    print("modified values are",list(set(taxaid) & set(taxaids)))
+
+
+    #convert DataFrame in .csv formate and assign to file_csv .
+    file_csv = df_merge.to_csv("final_merge.csv")
+    print ("csv file created as final_merge.csv")
+
+    #return file_csv
+    return file_csv, len(df_merge)
+
+
+
+
+#pass path of .dmp files in parameters.
+merge(names = 'taxadmp/names.dmp',nodes = 'taxadmp/nodes.dmp',merged = 'taxadmp/merged.dmp',delnodes = 'taxadmp/delnodes.dmp')