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only lowercase columns if at least one column affected, fixes #327 #332

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Merged
thomashopf merged 1 commit into from
Oct 23, 2025
Merged

only lowercase columns if at least one column affected, fixes #327 #332

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7 changes: 4 additions & 3 deletions evcouplings/align/protocol.py
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Original file line number Diff line number Diff line change
Expand Up @@ -943,10 +943,11 @@ def modify_alignment(focus_ali, target_seq_index, target_seq_id, region_start, *
min_col_cov /= 100

lc_cols = ali.count(ali._match_gap, axis="pos") > 1 - min_col_cov
ali = ali.lowercase_columns(lc_cols)

# if we remove columns, we have to update list of positions
pos_list = pos_list[~lc_cols]
if lc_cols.sum() > 0:
ali = ali.lowercase_columns(lc_cols)
# if we remove columns, we have to update list of positions
pos_list = pos_list[~lc_cols]
else:
lc_cols = None

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