diff --git a/python/obitools3/uri/decode.pyx b/python/obitools3/uri/decode.pyx index ad65318..be62b88 100644 --- a/python/obitools3/uri/decode.pyx +++ b/python/obitools3/uri/decode.pyx @@ -66,6 +66,7 @@ def open_dms_element(DMS dms, bytes path, if not path: return (dms,dms) + # TODO SHOULD READ AND RETURN PREFIX TO NEW TAXO WITHOUT CREATING ANYTHING # The URI targets a taxonomy # dms:dmspath/taxonomy/taxoname[/taxid] if path_parts[0]==b"taxonomy": @@ -282,20 +283,20 @@ def open_uri(uri, raise MalformedURIException('Malformed noquality argument in URI') if b"qualityformat" in qualifiers: - if qualifiers[b"qualityformat"][0]=="sanger": + if qualifiers[b"qualityformat"][0]==b"sanger": offset=33 - elif qualifiers[b"qualityformat"][0]=="solexa": + elif qualifiers[b"qualityformat"][0]==b"solexa": offset=64 else: try: - if config["obi"]["qualityformat"][0]=="sanger": + if config["obi"]["qualityformat"]==b"sanger": offset=33 - elif config["obi"]["qualityformat"][0]=="solexa": + elif config["obi"]["qualityformat"]==b"solexa": offset=64 #offset=config["obi"]["offset"] # TODO discuss except KeyError: offset=33 - + if b"header" in qualifiers: try: header=eval(qualifiers[b"header"][0])