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pfam_parser.py

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+import pandas as pd 
+import progressbar
+import gc
+import sys
+
+def pfam_parse(filename):
+    rlist=[]
+    try:
+        with open(filename) as file:
+            file.seek(0,0)
+            for line in progressbar.progressbar(file):
+                if line.startswith("#"):
+                    continue
+                temp_dict={}
+                x=[y for y in line.split(" ") if y !='']
+                if x[9] !="1":
+                    continue
+                temp_dict["gene_stable_id"]=x[3]
+                temp_dict["accession"]=x[1]
+                temp_dict["tlen"]=x[2]
+                temp_dict["qlen"]=x[5]
+                temp_dict["domain"]=x[0]
+                temp_dict["hmm_from"]=x[15]
+                temp_dict["hmm_to"]=x[16]
+                temp_dict["ali_from"]=x[17]
+                temp_dict["ali_to"]=x[18]
+                temp_dict["env_from"]=x[19]
+                temp_dict["env_to"]=x[20]
+                rlist.append(temp_dict)
+    except Exception as e:
+        print(e)
+        return pd.DataFrame()
+    print(len(rlist))
+    tdf=pd.DataFrame(rlist)
+    return tdf
+
+def main():
+    arg=sys.argv
+    fname_1=arg[-2]
+    fname_2=arg[-1]
+    df=pfam_parse(fname_1)
+    df.to_hdf("pfam_db_positive.h5",key="pfam_db_positive",mode="w")
+    df=""
+    gc.collect()
+    df=pfam_parse(fname_2)
+    df.to_hdf("pfam_db_negative.h5",key="pfam_db_negative",mode="w")
+    print("Pfam Databases Written Successfully :)")
+
+if __name__ == "__main__":
+    main()