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trim before simchar #11

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trim before simchar #11

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16 changes: 8 additions & 8 deletions alnvu/util.py
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,14 @@ def reformat(seqs,
else:
seqlist.append(cons)

if seqrange:
start, stop = seqrange
start -= 1 # seqrange is 1-indexed
elif trim_to:
start, stop = get_extent(get_seq_from_list(trim_to, seqlist).seq)
else:
start, stop = 0, len(tabulated)

if compare:
# replace bases identical to reference; make a copy of the
# sequence for comparison because the original sequences will
Expand All @@ -146,14 +154,6 @@ def reformat(seqs,

seqlist[i] = Seq(name, seqstr)

if seqrange:
start, stop = seqrange
start -= 1 # seqrange is 1-indexed
elif trim_to:
start, stop = get_extent(get_seq_from_list(trim_to, seqlist).seq)
else:
start, stop = 0, len(tabulated)

mask = []
for i, counts in enumerate(tabulated):
show = start <= i < stop
Expand Down