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Used the shquote function on the MAFFT add argument filename #452

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Mar 9, 2020
Merged

Used the shquote function on the MAFFT add argument filename #452

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4 changes: 2 additions & 2 deletions augur/align.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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 +
Expand Down Expand Up @@ -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)
Expand Down