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obi cat: Fixed the handling when concatenating views with dictionaries

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having different key sets
This commit is contained in:
Celine Mercier
2020-02-12 14:21:39 +01:00
parent dc9f897917
commit 219c0d6fdc
1 changed files with 18 additions and 1 deletions
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19
python/obitools3/commands/cat.pyx
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@ -86,7 +86,24 @@ def run(config):
if not remove_rev_qual:
Column.new_column(o_view, REVERSE_SEQUENCE_COLUMN, OBI_SEQ)
Column.new_column(o_view, REVERSE_QUALITY_COLUMN, OBI_QUAL, associated_column_name=REVERSE_SEQUENCE_COLUMN, associated_column_version=o_view[REVERSE_SEQUENCE_COLUMN].version)
# Initialize multiple elements columns
dict_cols = {}
for v in iview_list:
for coln in v.keys():
if v[coln].nb_elements_per_line > 1:
if coln not in dict_cols:
dict_cols[coln] = {}
dict_cols[coln]['eltnames'] = set(v[coln].elements_names)
dict_cols[coln]['nbelts'] = v[coln].nb_elements_per_line
dict_cols[coln]['obitype'] = v[coln].data_type_int
else:
dict_cols[coln]['eltnames'] = set(v[coln].elements_names + list(dict_cols[coln]['eltnames']))
dict_cols[coln]['nbelts'] = len(dict_cols[coln]['eltnames'])
for coln in dict_cols:
Column.new_column(o_view, coln, dict_cols[coln]['obitype'],
nb_elements_per_line=dict_cols[coln]['nbelts'], elements_names=list(dict_cols[coln]['eltnames']))
# Initialize the progress bar
pb = ProgressBar(total_len, config, seconde=5)