Commit d9ca56b0 authored by Alisa Muraveva's avatar Alisa Muraveva
Browse files

Some mistakes are fixed

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/mobile-2013@730 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
parent 1d940e80
......@@ -1352,6 +1352,7 @@ def _add_transcript_info(mutator, transcript, output):
descr, first, last_original, last_variant = \
util.protein_description(cds_length, protein_original,
protein_variant)
# Todo: Protein differences are not color-coded,
# use something like below in protein_description().
if protein_original[0]!="M":
......@@ -1967,7 +1968,7 @@ def star_subst(cds_original,protein, transcript, triplets, aa_dict_r, output, fl
protein=protein.tomutable()
genomic = transcript.CM.x2g(start*3, 0)
if flag:
output.addOutput('reference_exceptions', [str(start+1), str(start*3+1) + ".." + str(start*3+3), str(genomic+1) + ".." + str(genomic+3) , cds_original[start*3:start*3+3], protein[start] + ' (' + aa_dict_r[protein[start]] + ')', aa + ' (' + aa_dict_r[aa] + ')'])
output.addOutput('reference_exceptions', [str(start+1), str(start*3+1) + ".." + str(start*3+3), str(genomic+1) + ".." + str(genomic+3) , str(cds_original[start*3:start*3+3]), protein[start] + ' (' + aa_dict_r[protein[start]] + ')', aa + ' (' + aa_dict_r[aa] + ')'])
protein[start] = aa
protein=protein.toseq()
......
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