diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx index 09d61b3..2798d77 100755 --- a/python/obitools3/commands/import.pyx +++ b/python/obitools3/commands/import.pyx @@ -128,16 +128,12 @@ def run(config): NUC_SEQS_view = True else: raise NotImplementedError() - - get_quality = config["obi"]["noquality"] # Save basic columns in variables for optimization if NUC_SEQS_view : id_col = view[b"ID"] # TODO use macros or globals for column names def_col = view[b"DEFINITION"] seq_col = view[b"NUC_SEQ"] - if get_quality: - qual_col = view[b"QUALITY"] dcols = {} @@ -150,7 +146,13 @@ def run(config): id_col[i] = entry.id def_col[i] = entry.definition seq_col[i] = entry.seq - if get_quality : + # Check if there is a sequencing quality associated by checking the first entry # TODO haven't found a more robust solution yet + if i == 0: + get_quality = b"QUALITY" in entry + if get_quality: + Column.new_column(view, b"QUALITY", OBI_QUAL) + qual_col = view[b"QUALITY"] + if get_quality: qual_col[i] = entry.quality for tag in entry :