From 3b10d6bd3cf6e2bf7be2283e08e513f34f8574ee Mon Sep 17 00:00:00 2001 From: Travis Harrison Date: Tue, 19 Dec 2017 11:42:50 -0600 Subject: [PATCH] iupac update --- bin/seq_length_stats.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/bin/seq_length_stats.py b/bin/seq_length_stats.py index 47e17d8..1746b0c 100755 --- a/bin/seq_length_stats.py +++ b/bin/seq_length_stats.py @@ -36,13 +36,13 @@ ] IUPAC_AA = [ - 'a','b','c','d','e','f','g','h','i','k','l','m','n','p','q','r','s','t','v','w','x','y','z', - 'A','B','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','X','Y','Z', - ' ', '\n' + 'a','b','c','d','e','f','g','h','i','j','k','l','m','n','o','p','q','r','s','t','u','v','w','x','y','z', + 'A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z', + '*', ' ', '\n' ] IUPAC_AA_STRICT = [ - 'A','B','C','D','E','F','G','H','I','K','L','M','N','P','Q','R','S','T','V','W','X','Y','Z' + 'A','B','C','D','E','F','G','H','I','J','K','L','M','N','O','P','Q','R','S','T','U','V','W','X','Y','Z' ] def sum_map(aMap): @@ -112,7 +112,7 @@ def main(args): parser.add_option("-j", "--json", dest="json", default=False, action="store_true", help="Output stats in json format, default is tabbed text") parser.add_option("-t", "--type", dest="type", default="fasta", help="Input file type. Must be fasta or fastq [default 'fasta']") parser.add_option("-p", "--protein", dest="protein", default=False, action="store_true", help="Input file is Protein sequences [default is DNA/RNA]") - parser.add_option("-n", "--n_percent", dest="n_percent", default=100, help="Percent of sequence that is Ns for it to be counted [default is 100]") + parser.add_option("-x", "--x_percent", dest="x_percent", default=100, help="Percent of protein sequence that is Xs for it to be counted [default is 100]") parser.add_option("-l", "--length_bin", dest="len_bin", metavar="FILE", default=None, help="File to place length bins [default is no output]") parser.add_option("-g", "--gc_percent_bin", dest="gc_bin", metavar="FILE", default=None, help="File to place % gc bins [default is no output]") parser.add_option("-f", "--fast", dest="fast", default=False, action="store_true", help="Fast mode, only calculate length stats")