diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx index 04dd8df..09d61b3 100755 --- a/python/obitools3/commands/import.pyx +++ b/python/obitools3/commands/import.pyx @@ -105,7 +105,6 @@ def run(config): output = open_uri(config['obi']['outputURI'], input=False, newviewtype=v) - #quality=get_quality) # TODO if output is None: raise Exception("Could not create output view") @@ -129,33 +128,28 @@ 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 = {} - + i = 0 for entry in entries : pb(i) - - if NUC_SEQS_view : - - # Check if there is a sequencing quality associated # TODO - 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 NUC_SEQS_view: id_col[i] = entry.id def_col[i] = entry.definition seq_col[i] = entry.seq - if get_quality : qual_col[i] = entry.quality