Camelia, the Perl 6 bug

IRC log for #bioperl, 2010-07-18

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All times shown according to UTC.

Time Nick Message
08:01 bag joined #bioperl
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18:16 deafferret hmm... so I'll have millions of features across lots of assemblies of different organisms each with lots of chromosomes
18:17 deafferret do I want one big SQLite database, or one per assembly + chromosome?
18:17 deafferret since I want to both GBrowse and query
18:17 deafferret "show me all the miRNA-1290s that are in the 5'UTRs of certain mRNAs
18:17 deafferret "
18:18 deafferret and I want to kick out gff for attaching to the public ensembl, or UCSC, etc...
18:19 deafferret ... and be done today   :)
18:19 deafferret hopes Bio::DB::SeqFeature::Store::DBI::SQLite  is the right playbook
18:44 bag joined #bioperl
19:41 deafferret is there some methodology for searching for all overlapping features?  "show me all the features foo overlapping features bar"
21:36 brandi joined #bioperl
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22:01 deafferret oh dear. Bio::DB::SeqFeature::Store::DBI::SQLite  + bp_seqfeature_gff3.PLS  fails to round-trip
22:01 deafferret 4 hours down the drain   :(
22:01 deafferret should have rolled my own from the beginning apparently

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