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arq5x / gemini

a lightweight db framework for exploring genetic variation.
http://gemini.readthedocs.org
MIT License
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gemini query error with --header option #241

Closed m1m0r1 closed 10 years ago

m1m0r1 commented 10 years ago

I encountered following errors which is not occurred when using the command without --header option.

$ gemini query --header -q 'select chrom,start,end,gene,transcript,is_exonic,is_coding,is_lof,exon,codon_change,aa_change,aa_length,biotype,impact,impact_severity from variants limit 30' test.db Traceback (most recent call last): File "/share1/home/ig/.virtualenvs/gemini/bin/gemini", line 5, in gemini.gemini_main.main() File "/share1/home/ig/.virtualenvs/gemini/lib/python2.7/site-packages/gemini/gemini_main.py", line 786, in main args.func(parser, args) File "/share1/home/ig/.virtualenvs/gemini/lib/python2.7/site-packages/gemini/gemini_query.py", line 128, in query run_query(args) File "/share1/home/ig/.virtualenvs/gemini/lib/python2.7/site-packages/gemini/gemini_query.py", line 115, in run_query if args.use_header and gq.header: File "/share1/home/ig/.virtualenvs/gemini/lib/python2.7/site-packages/gemini/GeminiQuery.py", line 389, in header [col for col in OrderedSet(self.all_columns_orig) AttributeError: 'GeminiQuery' object has no attribute 'all_columns_orig' |----|

m1m0r1 commented 10 years ago

I forgot to attach the version of gemini

$ gemini --version gemini 0.6.3.2

arq5x commented 10 years ago

Thanks for reporting this. I will try to get a fix in as soon as I am able, but it might be a bit given the holidays.

arq5x commented 10 years ago

I just pushed a fix for this, sorry for the difficulty! You can pull in the changes with:

gemini update --devel