From c655354a4217595f654ea0de602f9b01580b63e2 Mon Sep 17 00:00:00 2001 From: Auden Cote-L'Heureux <52716489+AudenCote@users.noreply.github.com> Date: Tue, 19 Dec 2023 13:28:40 -0500 Subject: [PATCH] Update and rename faralog.py to gappiness.py --- Utilities/for_MSAs/{faralog.py => gappiness.py} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename Utilities/for_MSAs/{faralog.py => gappiness.py} (97%) diff --git a/Utilities/for_MSAs/faralog.py b/Utilities/for_MSAs/gappiness.py similarity index 97% rename from Utilities/for_MSAs/faralog.py rename to Utilities/for_MSAs/gappiness.py index 0091f60..426e837 100644 --- a/Utilities/for_MSAs/faralog.py +++ b/Utilities/for_MSAs/gappiness.py @@ -38,7 +38,7 @@ def faralog_gaps(): split = [] #reading the fasta files with Biopython (looping each sequence in a file and populating the empty name and seq lists). for x in SeqIO.parse(args.alignment + '/' + file, "fasta"): - if x.id.startswith(args.code): + if (args.code != None and x.id.startswith(args.code)) or args.code == None: name.append(x.id) seq.append(x.seq) seq_len.append(len(x.seq))