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import command a bit modified for tests

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This commit is contained in:
Celine Mercier
2016-04-26 14:29:54 +02:00
parent 366264828e
commit a6c8d35491
1 changed files with 11 additions and 9 deletions
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16
python/obitools3/commands/import.pyx
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@ -92,9 +92,7 @@ def addOptions(parser):
def run(config): def run(config):
#pb = ProgressBar(1000,config,seconde=1) pb = ProgressBar(35000000,config,seconde=5)
print(config)
inputs = uopen(config['import']['filename']) inputs = uopen(config['import']['filename'])
@ -107,6 +105,9 @@ def run(config):
else: else:
raise RuntimeError('No file format specified') raise RuntimeError('No file format specified')
# Temporary way to handle NA values
NA_list = ["nan"]
# Create DMS # Create DMS
d = OBIDMS(config['obi']['defaultdms']) d = OBIDMS(config['obi']['defaultdms'])
@ -115,17 +116,18 @@ def run(config):
i = 0 i = 0
for seq in iseq: for seq in iseq:
#pb(i) pb(i)
view[i].set_id(seq['id']) view[i].set_id(seq['id'])
view[i].set_definition(seq['definition']) view[i].set_definition(seq['definition'])
view[i].set_sequence(seq['sequence']) view[i].set_sequence(seq['sequence'])
# for tag in seq['tags'] : for tag in seq['tags'] :
#print(tag, seq['tags'][tag]) #print(tag, seq['tags'][tag])
# view[i][tag] = seq['tags'][tag] #if seq['tags'][tag] not in NA_list :
view[i][tag] = seq['tags'][tag]
i+=1 i+=1
print(view) print(view)
print(view.__repr__()) # print(view.__repr__())
view.save_and_close() view.save_and_close()
d.close() d.close()