diff --git a/python/obitools3/commands/import.pyx b/python/obitools3/commands/import.pyx index c9d4ce0..7df883b 100644 --- a/python/obitools3/commands/import.pyx +++ b/python/obitools3/commands/import.pyx @@ -92,10 +92,8 @@ def addOptions(parser): def run(config): - #pb = ProgressBar(1000,config,seconde=1) - - print(config) - + pb = ProgressBar(35000000,config,seconde=5) + inputs = uopen(config['import']['filename']) if config['import']['seqinformat']=='fasta': @@ -107,6 +105,9 @@ def run(config): else: raise RuntimeError('No file format specified') + # Temporary way to handle NA values + NA_list = ["nan"] + # Create DMS d = OBIDMS(config['obi']['defaultdms']) @@ -115,17 +116,18 @@ def run(config): i = 0 for seq in iseq: - #pb(i) + pb(i) view[i].set_id(seq['id']) view[i].set_definition(seq['definition']) view[i].set_sequence(seq['sequence']) -# for tag in seq['tags'] : -# print(tag, seq['tags'][tag]) -# view[i][tag] = seq['tags'][tag] + for tag in seq['tags'] : + #print(tag, seq['tags'][tag]) + #if seq['tags'][tag] not in NA_list : + view[i][tag] = seq['tags'][tag] i+=1 print(view) - print(view.__repr__()) + # print(view.__repr__()) view.save_and_close() d.close()