Cython API: compiling but not working
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@ -2,7 +2,7 @@ from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
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from obitools3.files.universalopener cimport uopen
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from obitools3.parsers.fasta import fastaIterator
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from obitools3.parsers.fastq import fastqIterator
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from obitools3.obidms._obidms import OBIDMS
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from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
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import time
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@ -109,22 +109,22 @@ def run(config):
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d = OBIDMS(config['obi']['defaultdms'])
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# Create view
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view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
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i = 0
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for seq in iseq:
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pb(i)
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view[i].id = seq['id']
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view[i].definition = seq['definition']
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view[i].nuc_seq = seq['sequence']
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if get_quality :
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view[i].quality = seq['quality']
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for tag in seq['tags'] :
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view[i][tag] = seq['tags'][tag]
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i+=1
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#print(view.__repr__())
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view.close()
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# view = d.new_view(config['import']['destview'], view_type=view_type, quality_column=get_quality)
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#
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# i = 0
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# for seq in iseq:
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# pb(i)
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# view[i].id = seq['id']
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# view[i].definition = seq['definition']
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# view[i].nuc_seq = seq['sequence']
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# if get_quality :
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# view[i].quality = seq['quality']
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# for tag in seq['tags'] :
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# view[i][tag] = seq['tags'][tag]
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# i+=1
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#
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# #print(view.__repr__())
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#
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# view.close()
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d.close()
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