# HG changeset patch
# User Jan Kanis <jan.code@jankanis.nl>
# Date 1406816076 -7200
# Node ID 2729c2326235cf92fdbf99642a19b7bb3283fe28
# Parent  591dc9c248247023e04e5b1dca3f6be0731db935
Fix for Rikilt issue 13

Hit e-value and identity% should be taken from the hsp with the highest
bit score. Previously each of these values was calculated independently.

Also use arrays for cover calculation instead of python lists and
refactor the hit_info() code a bit.

diff -r 591dc9c24824 -r 2729c2326235 blast2html.py
--- a/blast2html.py	Thu Jul 31 13:26:34 2014 +0200
+++ b/blast2html.py	Thu Jul 31 16:14:36 2014 +0200
@@ -16,6 +16,7 @@
 from os import path
 from itertools import repeat
 from collections import defaultdict, namedtuple
+from array import array
 import glob
 import argparse
 from lxml import objectify
@@ -327,23 +328,22 @@
         for hit in hits(result):
             hsps = hit.Hit_hsps.Hsp
 
-            cover = [False] * query_length
+            cover = array('B', [0]) * query_length
             for hsp in hsps:
-                cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = repeat(True, blastxml_len(hsp))
-            cover_count = cover.count(True)
+                cover[hsp['Hsp_query-from']-1 : int(hsp['Hsp_query-to'])] = array('B', [1]) * blastxml_len(hsp)
+            cover_count = cover.count(1)
 
-            def hsp_val(path):
-                return (float(hsp[path]) for hsp in hsps)
+            best_hsp = max(hsps, key=lambda h: h['Hsp_bit-score'])
 
             yield dict(hit = hit,
                        title = firsttitle(hit),
-                       maxscore = "{0:.1f}".format(max(hsp_val('Hsp_bit-score'))),
-                       totalscore = "{0:.1f}".format(sum(hsp_val('Hsp_bit-score'))),
-                       cover = "{0:.0%}".format(cover_count / query_length),
-                       e_value = "{0:.4}".format(float(min(hsp_val('Hsp_evalue')))),
-                       # FIXME: is this the correct formula vv?
+                       maxscore = format(float(best_hsp['Hsp_bit-score']), '.1f'),
+                       e_value = format(float(best_hsp.Hsp_evalue), '.4'),
                        # float(...) because non-flooring division doesn't work with lxml elements in python 2.6
-                       ident = "{0:.0%}".format(float(min(float(hsp.Hsp_identity) / blastxml_len(hsp) for hsp in hsps))))
+                       ident = format(float(best_hsp.Hsp_identity) / blastxml_len(best_hsp), '.0%'),
+                       totalscore = format(sum(hsp['Hsp_bit-score'] for hsp in hsps), '.1f'),
+                       cover = format(cover_count / query_length, '.0%'),
+                  )
 
     @filter
     def genelink(self, hit, text=None, text_from='hitid', cssclass=None, display_nolink=True):