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Added properties for Nuc_Seq cython classes (and updated commands using

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them)
This commit is contained in:
Celine Mercier
2016-11-08 16:59:32 +01:00
parent b5b889c4a2
commit 51b23915ca
4 changed files with 89 additions and 90 deletions
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15
python/obitools3/commands/import.pyx
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@ -90,7 +90,7 @@ def addOptions(parser):
# TODO: Handling of NA values
def run(config):
pb = ProgressBar(35000000, config, seconde=5)
pb = ProgressBar(10000, config, seconde=5) # TODO should be number of records in file
inputs = uopen(config['import']['filename'])
@ -107,25 +107,24 @@ def run(config):
# Create DMS
d = OBIDMS(config['obi']['defaultdms'])
# Create view
view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
i = 0
for seq in iseq:
pb(i)
view[i].set_id(seq['id'])
view[i].set_definition(seq['definition'])
view[i].set_sequence(seq['sequence'])
view[i].id = seq['id']
view[i].definition = seq['definition']
view[i].nuc_seq = seq['sequence']
if get_quality :
view[i].set_quality(seq['quality'])
view[i].quality = seq['quality']
for tag in seq['tags'] :
view[i][tag] = seq['tags'][tag]
i+=1
print(view.__repr__())
#print(view.__repr__())
view.close()
d.close()
print("Done.")