The color of noncanonical amino acids was changed and the column was added to...

The color of noncanonical amino acids was changed and the column was added to 'Translation exceptions for predicted protein' table 

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@740 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

mutalyzer/templates/base/css/style.css

@@ -325,7 +325,7 @@ pre.monoseq {
     font-weight: bold;
 }
 .monoseq-annotation-1 {
-    background: #8096B2 ;
+    background: #002E65 ;
     font-weight: bold;
     color: white;
 }

mutalyzer/templates/check.html

@@ -226,6 +226,7 @@
                   <td>Triplet</td>
                   <td>Original amino acid</td>
                   <td>Substituted amino acid</td>
+                  <td>Reference protein contains the same substitution</td>
                 </tr>
                 <tr tal:repeat = "i predicted_exceptions">
                     <td tal:content = "repeat/i/number"></td>

mutalyzer/variantchecker.py

@@ -1325,8 +1325,8 @@ def _add_transcript_info(mutator, transcript, output):
         if '*' in protein_original[:-1]:
             output.addMessage(__file__, 3, 'ESTOP',
                               'In frame stop codon.')   
-        protein_variant = cds_variant.translate(table = transcript.txTable)                                 
-        protein_variant, result = substitute_variant_prot(cds_variant, protein_variant, triplets, transcript,output, True)
+        protein_variant = cds_variant.translate(table = transcript.txTable)                              
+        protein_variant, result = substitute_variant_prot(cds_variant, protein_variant, triplets, transcript,output,True,res)
         if result:
              output.addMessage(__file__, 2, 'WSUBST',
                               ' The noncanonical amino acids were found and substituted in \
@@ -1833,7 +1833,7 @@ def check_variant(description, output):
                     return
                 protein_variant = cds_variant.translate(table = transcript.txTable)                         
                 
-                protein_variant, result = substitute_variant_prot(cds_variant, protein_variant, triplets, transcript, output, False)
+                protein_variant, result = substitute_variant_prot(cds_variant, protein_variant, triplets, transcript, output, False, res)
                 #add Selenocysteine recognition. [see substitute_variant function]
                 #protein_variant = substitute_variant_prot(cds_variant, protein_variant, triplets, True)    
                 #&&&
@@ -1994,7 +1994,7 @@ def star_subst(cds_original,protein, transcript, triplets, aa_dict_r, output, fl
                 protein=protein.toseq()
  
     return protein.split("*")[0], res 
-def substitute_variant_prot(nucl_seq, prot_seq, triplets, transcript, output, flag, Sec = False):
+def substitute_variant_prot(nucl_seq, prot_seq, triplets, transcript, output, flag, start_original, Sec = False):
     '''This function return a changed protein. Amino acids are substituted according to triplets dictionary. 
        Unfortunately, the function does not check context around substituted amino_acid, but it has that possibility in future'''
     result = []
@@ -2011,8 +2011,12 @@ def substitute_variant_prot(nucl_seq, prot_seq, triplets, transcript, output, fl
                      #  prot[i] =  triplets[triplet]
                     
                 if flag:
-                    genomic = transcript.CM.x2g(i*3, 0)                
-                    exceptions.append([i+1, str(i*3+1) + ".." + str(i*3+3), str(genomic+1) + ".." + str(genomic+3), triplet, prot[i] + ' (' + aa_dict_r[prot[i]] + ')', triplets[triplet] + ' (' + aa_dict_r[triplets[triplet]] + ')'])
+                    genomic = transcript.CM.x2g(i*3, 0) 
+                    if i in start_original:               
+                        exceptions.append([i+1, str(i*3+1) + ".." + str(i*3+3), str(genomic+1) + ".." + str(genomic+3), triplet, prot[i] + ' (' + aa_dict_r[prot[i]] + ')', triplets[triplet] + ' (' + aa_dict_r[triplets[triplet]] + ')', 'Yes'])
+                    else:
+                          exceptions.append([i+1, str(i*3+1) + ".." + str(i*3+3), str(genomic+1) + ".." + str(genomic+3), triplet, prot[i] + ' (' + aa_dict_r[prot[i]] + ')', triplets[triplet] + ' (' + aa_dict_r[triplets[triplet]] + ')'])
+
                 prot[i] =  triplets[triplet]
     prot = prot.toseq()   
     prot = prot.split("*")[0]