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  • #61

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Opened Feb 08, 2021 by Gabriele Cananzi@gabrielecananzi

obiconvert issue

Hi everyone, I am having this issue with obiconvert, hope someone could help me!

obiconvert --embl -t ./TAXO --ecopcrdb-output=embl_last ./EMBL/*.dat Reading taxonomy dump file... List all taxonomy rank... Traceback (most recent call last): File "/usr/bin/obiconvert", line 43, in writer = sequenceWriterGenerator(options) File "/usr/lib/python3/dist-packages/obitools/format/options.py", line 364, in sequenceWriterGenerator writer=EcoPCRDBSequenceWriter(options) File "/usr/lib/python3/dist-packages/obitools/ecopcr/sequence.py", line 72, in init self._taxonomy= loadTaxonomyDatabase(options) File "/usr/lib/python3/dist-packages/obitools/ecopcr/options.py", line 79, in loadTaxonomyDatabase taxonomy = TaxonomyDump(options.taxdump) File "/usr/lib/python3/dist-packages/obitools/ecopcr/taxonomy.py", line 420, in init self._readNodeTable('%s/nodes.dmp' % taxdir) File "/usr/lib/python3/dist-packages/obitools/ecopcr/taxonomy.py", line 496, in _readNodeTable rankidx = dict(map(None,ranks,range(len(ranks)))) TypeError: 'NoneType' object is not callable Exception ignored in: <function EcoPCRDBSequenceWriter.del at 0x7fa33985d310> Traceback (most recent call last): File "/usr/lib/python3/dist-packages/obitools/ecopcr/sequence.py", line 180, in del self.close() File "/usr/lib/python3/dist-packages/obitools/ecopcr/sequence.py", line 149, in close self._file.seek(0,0) AttributeError: 'EcoPCRDBSequenceWriter' object has no attribute '_file'

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Reference: obitools/obitools#61