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  • #18

Closed
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Opened Dec 22, 2015 by Nicholas Lim@chizarel

obiconvert: GenBank/FASTA input to ecoPCR database

I'm attempting to convert sequences retrieved from GenBank to an ecoPCR database. I've tried both .gb and FASTA (with taxids in sequence headers) formats, and also tried using both the unzipped NCBI taxdump and the binary taxonomy database generated using obitaxonomy. However, it keeps getting stuck with the following:

main : 00:01:09Traceback (most recent call last): File "/home/evolab1/obitools/OBITools-1.2.0/export/bin/obiconvert", line 52, in writer(entry) File "/home/evolab1/obitools/OBITools-1.2.0/local/lib/python2.7/site-packages/obitools/format/options.py", line >371, in sequenceWriter writer.put(sequence) File "/home/evolab1/obitools/OBITools-1.2.0/local/lib/python2.7/site-packages/obitools/ecopcr/sequence.py", line >173, in put self._file.write(self._ecoSeqPacker(sequence)) File "/home/evolab1/obitools/OBITools-1.2.0/local/lib/python2.7/site-packages/obitools/ecopcr/sequence.py", line >124, in _ecoSeqPacker taxon=self._taxonomy.findIndex(seq['taxid']) File "/home/evolab1/obitools/OBITools-1.2.0/local/lib/python2.7/site-packages/obitools/ecopcr/taxonomy.py", line >53, in findIndex return self._index[taxid] KeyError: 1774270

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Reference: obitools/obitools#18