From a898486701ffdf1c88586f4501879267af18430e Mon Sep 17 00:00:00 2001 From: carlosp420 Date: Thu, 16 Apr 2015 11:48:56 +0300 Subject: [PATCH] trimming seqs --- voseq/create_dataset/utils.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/voseq/create_dataset/utils.py b/voseq/create_dataset/utils.py index f72b400c..36c316d1 100644 --- a/voseq/create_dataset/utils.py +++ b/voseq/create_dataset/utils.py @@ -64,7 +64,8 @@ def convert_lists_to_dataset(self, partitions): if aa_sequence.strip() == '': self.warnings.append("Sequence for %s %s was empty" % (voucher_code, this_gene)) - out += [line[0] + '\n' + sequence + '\n'] + sequence = strip_question_marks(sequence)[0] + out += [line[0] + '\n' + sequence.replace('?', 'N') + '\n'] aa_out += [line[0] + '\n' + aa_sequence + '\n'] dataset_str = ''.join(out)