diff --git a/CHANGES.rst b/CHANGES.rst index d72b5425341820785d5bb98206b19f5e1a5b0bb2..e938eed49c1290971145ab0b059fdb84eac9025a 100644 --- a/CHANGES.rst +++ b/CHANGES.rst @@ -17,6 +17,8 @@ Release date to be decided. <https://git.lumc.nl/mutalyzer/mutalyzer/merge_requests/25>`_). - Don't crash on mail errors in the batch scheduler (`GitLab#30 <https://git.lumc.nl/mutalyzer/mutalyzer/issues/30>`_). +- Fix importing transcript mappings from UCSC database (`GitLab#9 + <https://git.lumc.nl/mutalyzer/mutalyzer/issues/9>`_). Version 2.0.3 diff --git a/mutalyzer/mapping.py b/mutalyzer/mapping.py index 11e058997182252b01d75ea1b0586cb555347d18..ba4d11102919c0b384511ca24e61494991fa0c43 100644 --- a/mutalyzer/mapping.py +++ b/mutalyzer/mapping.py @@ -789,17 +789,15 @@ class Converter(object) : #Converter -# Todo: This seems broken at the moment. -# Todo: Correct handling of string encodings. def import_from_ucsc_by_gene(assembly, gene): """ Import transcript mappings for a gene from the UCSC. - - .. todo: Also report how much was added/updated. """ connection = MySQLdb.connect(user='genome', host='genome-mysql.cse.ucsc.edu', - db=assembly.alias) + db=assembly.alias, + charset='utf8', + use_unicode=True) query = """ SELECT DISTINCT @@ -811,7 +809,7 @@ def import_from_ucsc_by_gene(assembly, gene): AND acc = mrnaAcc AND name2 = %s """ - parameters = gene + parameters = gene, cursor = connection.cursor() cursor.execute(query, parameters)