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uniq: improved progress bar of second browsing

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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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9
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("") print("")
logger("info", "Second browsing through the input") logger("info", "Second browsing through the input")
# Initialize the progress bar # Initialize the progress bar
pb = ProgressBar(len(uniques), seconde=5) pb = ProgressBar(len(view), seconde=5)
o_idx = 0 o_idx = 0
total_treated = 0
for unique_id in uniques : for unique_id in uniques :
PyErr_CheckSignals() PyErr_CheckSignals()
pb(o_idx)
merged_sequences = uniques[unique_id] merged_sequences = uniques[unique_id]
@ -453,6 +453,7 @@ 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:
pb(total_treated)
i_id = i_id_col[i_idx] i_id = i_id_col[i_idx]
i_seq = view[i_idx] i_seq = view[i_idx]
@ -505,6 +506,8 @@ cdef uniq_sequences(View_NUC_SEQS view, View_NUC_SEQS o_view, ProgressBar pb, di
and key not in merged_dict : and key not in merged_dict :
o_seq[key] = None o_seq[key] = None
total_treated += 1
# Write merged dicts # Write merged dicts
for mkey in merged_dict: for mkey in merged_dict:
if mkey in str_merged_cols: 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_count_col[o_idx] = o_count
o_idx += 1 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) # 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: if QUALITY_COLUMN in view: