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uniq: improved progress bar of second browsing

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This commit is contained in:
Celine Mercier
2020-06-09 14:36:02 +02:00
parent 8776ce22e6
commit aa836b2ace
1 changed files with 8 additions and 5 deletions
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13
python/obitools3/commands/uniq.pyx
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@ -419,12 +419,12 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
print("")
logger("info", "Second browsing through the input")
# Initialize the progress bar
pb = ProgressBar(len(uniques), seconde=5)
pb = ProgressBar(len(view), seconde=5)
o_idx = 0
total_treated = 0
for unique_id in uniques :
PyErr_CheckSignals()
pb(o_idx)
merged_sequences = uniques[unique_id]
@ -453,7 +453,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
merged_dict[mkey] = {}
for i_idx in merged_sequences:
pb(total_treated)
i_id = i_id_col[i_idx]
i_seq = view[i_idx]
@ -504,7 +505,9 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
if key != COUNT_COLUMN and key != ID_COLUMN and key != NUC_SEQUENCE_COLUMN and key in o_seq and o_seq[key] != i_seq[key] \
and key not in merged_dict :
o_seq[key] = None
total_treated += 1
# Write merged dicts
for mkey in merged_dict:
if mkey in str_merged_cols:
@ -526,7 +529,7 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
o_count_col[o_idx] = o_count
o_idx += 1
pb(len(uniques), force=True)
pb(len(view), force=True)
# Deletes quality columns if there is one because the matching between sequence and quality will be broken (quality set to NA when sequence not)
if QUALITY_COLUMN in view: