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OBITools
OBITools3
Commits
9100e148
Commit
9100e148
authored
Jul 03, 2020
by
Celine Mercier
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obi uniq: quick fix for bug where some sequences are not correctly
dereplicated
parent
ccda0661
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2 deletions
+4
-2
uniq.pyx
python/obitools3/commands/uniq.pyx
+3
-1
version.py
python/obitools3/version.py
+1
-1
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python/obitools3/commands/uniq.pyx
View file @
9100e148
...
@@ -307,7 +307,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
...
@@ -307,7 +307,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
for x in categories :
for x in categories :
catl.append(i_seq[x])
catl.append(i_seq[x])
unique_id = tuple(catl) + (i_seq_col.get_line_idx(i),)
unique_id = tuple(catl) + (i_seq_col[i],)
#unique_id = tuple(catl) + (i_seq_col.get_line_idx(i),)
#unique_id = tuple(i_seq[x] for x in categories) + (seq_col.get_line_idx(i),) # The line that cython can't read properly
#unique_id = tuple(i_seq[x] for x in categories) + (seq_col.get_line_idx(i),) # The line that cython can't read properly
if unique_id in uniques:
if unique_id in uniques:
...
@@ -453,6 +454,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
...
@@ -453,6 +454,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
merged_dict[mkey] = {}
merged_dict[mkey] = {}
for i_idx in merged_sequences:
for i_idx in merged_sequences:
PyErr_CheckSignals()
pb(total_treated)
pb(total_treated)
i_id = i_id_col[i_idx]
i_id = i_id_col[i_idx]
...
...
python/obitools3/version.py
View file @
9100e148
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