use unwinding operator to parse blast output

source/_static/code/parse_blast.py

 from operator import itemgetter
 from collections import namedtuple
 
-Hit = namedtuple("Hit" ,"id percent identity align_len mis_num, open_gap_num\
-                  query_start, query_end, subject_start, subject_end, E_value, HSP_bit_score")
+Hit = namedtuple("Hit", ("query", "subject", "identity", "align_len", "mis_num", "open_gap_num",
+                  "query_start", "query_end", "subject_start", "subject_end", "E_value", "HSP_bit_score"))
 
 def parse_blast_output(input_file):
     """
@@ -14,13 +14,13 @@ def parse_blast_output(input_file):
     with open(input_file, 'r') as infile:
         table = []
         for line in infile:
-            col = line.split('\t')
+            query, subject, identity, *stuff, bit_score = line.split('\t')
             try:
-                col[2] = float(col[2])
+                identity = float(identity)
             except ValueError as err:
                 raise RuntimeError("error in parsing {} : {}".format(input_file, err))
-            col[-1] = col[-1][:-1]
-            table.append(col)
+            bit_score = bit_score.strip()
+            table.append([query, subject, identity, *stuff, bit_score])
     return table
 
 
@@ -42,10 +42,8 @@ def write_blast_output(hits, output_file):
    
 if __name__ == '__main__':
     table_hits = parse_blast_output('blast2.txt')
-    #table_hits = parse_blast_output('blast.txt')
-    table_sorted = sorted(table_hits, key = itemgetter(2), reverse = True)
+    table_sorted = sorted(table_hits, key=itemgetter(2), reverse=True)
     # alternative
     # table_sorted = sorted(table, key = lambda x : x[2], reversed = True)
     write_blast_output(table_hits, 'blast_sorted.txt')  
-   
-         
+