From 7d9c962ab12ebd97a69aa7b80d9b5732e271f59f Mon Sep 17 00:00:00 2001 From: Cameron Devine Date: Fri, 6 Mar 2020 14:42:49 -0800 Subject: [PATCH] Used the shquote function on the mafft add argument filename --- augur/align.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/augur/align.py b/augur/align.py index 40ec62b1e..c8146ae65 100644 --- a/augur/align.py +++ b/augur/align.py @@ -176,7 +176,7 @@ def read_reference(ref_fname): def generate_alignment_cmd(method, nthreads, existing_aln_fname, seqs_to_align_fname, aln_fname, log_fname): if method=='mafft': if existing_aln_fname: - cmd = "mafft --add %s --keeplength --reorder --anysymbol --thread %d %s 1> %s 2> %s"%(seqs_to_align_fname, nthreads, shquote(existing_aln_fname), shquote(aln_fname), shquote(log_fname)) + cmd = "mafft --add %s --keeplength --reorder --anysymbol --thread %d %s 1> %s 2> %s"%(shquote(seqs_to_align_fname), nthreads, shquote(existing_aln_fname), shquote(aln_fname), shquote(log_fname)) else: cmd = "mafft --reorder --anysymbol --thread %d %s 1> %s 2> %s"%(nthreads, shquote(seqs_to_align_fname), shquote(aln_fname), shquote(log_fname)) print("\nusing mafft to align via:\n\t" + cmd + @@ -264,7 +264,7 @@ def add(name): if not sample: # allows false-like values (e.g. always provide existing_alignment, allowing # the default which is `False`) - continue + continue elif type(sample) == dict: for s in sample: add(s)