# HG changeset patch
# User sanbi-uwc
# Date 1658421796 0
# Node ID 31ca16290d4f64c24d80d9ef632d49d743200240
# Parent  9105ec01691169b101ff851ac9d8d597ce26ac01
planemo upload for repository https://github.com/pvanheus/polio_report commit a99e10fec2fac5aae70974c977eb3b362a1a8429-dirty

diff -r 9105ec016911 -r 31ca16290d4f assess_alignment.py
--- a/assess_alignment.py	Tue Jul 19 11:57:09 2022 +0000
+++ b/assess_alignment.py	Thu Jul 21 16:43:16 2022 +0000
@@ -106,7 +106,7 @@
         if state == "M":
             # for mismatch store [pos_in_genome, pos_in_vp1, reference_base, sequenced_base]
             mismatch_list.append(
-                [i, i - offset, reference["align"][i], mismatch_bases[i]]
+                [i, i - offset + 1, reference["align"][i], mismatch_bases[i]]
             )
     return [conflicts, matches, mismatches, mismatch_list]
 
@@ -153,9 +153,10 @@
     args = parser.parse_args()
 
     offsets = {
-        "poliovirus1sabin": 2480,
-        "poliovirus2sabin": 2482,
-        "poliovirus3sabin": 2477,
+        # these are in 0-based coordinates, so off-by-one from NCBI 1-based coordinates
+        "poliovirus1sabin": 2479, # V01150
+        "poliovirus2sabin": 2481, # AY184220
+        "poliovirus3sabin": 2478, # X00925
     }
 
     lengths = {
@@ -181,6 +182,7 @@
             best_match_mismatch_list = mismatch_list
             best_match_quality = quality
             best_match_reference = dataset_name
+            percent_mismatches = round(min_mismatches / lengths[best_match_reference] * 100, 2)
 
     info = {
         "sample_name": args.sample_name,
@@ -188,5 +190,6 @@
         "mismatches": min_mismatches,
         "mismatch_list": best_match_mismatch_list,
         "quality": best_match_quality,
+        "perc_mismatches": percent_mismatches
     }
     json.dump(info, open(args.output_filename, "w"))
diff -r 9105ec016911 -r 31ca16290d4f assess_poliovirus_alignment.xml
--- a/assess_poliovirus_alignment.xml	Tue Jul 19 11:57:09 2022 +0000
+++ b/assess_poliovirus_alignment.xml	Thu Jul 21 16:43:16 2022 +0000
@@ -1,4 +1,4 @@
-<tool id="assess_poliovirus_alignment" name="Assess poliovirus alignment" version="0.1.0+galaxy1" profile="21.05">
+<tool id="assess_poliovirus_alignment" name="Assess poliovirus alignment" version="0.2.0+galaxy0" profile="21.05">
     <requirements>
         <requirement type="package" version="3.9">python</requirement>
     </requirements>