Gave sqlite own module
Created drivers for command that only outputs a protein group lookup db
Added protein group lookup command
Made table creating in own method on DB object
Forgot two lines of imports due to not grepping carefully enough
Could not move output because had not set class variable
Cosmetics
Own reader for protein table. Probably unneccessary but naming is clear
Created protein table modifier executable. It can now add some protein data to a table of protein accessions
Chmod and added writer for protein table
Fixed an import
Actually include tables for descriptions
Testing prottable add protein data
Indexing for more speed
Copy sql lookup to workdir before running. This slows things down due to the copy, but there is a major win on nfs-mounted sqlite lookups
Found a bug which causes last proteingroup in table to never be stored
Split up protein grouping into two commands. Lookup creation and adding groups to PSM table
Added protgroupdb to command line options in protein grouping
Bugs in protein grouping after splitting from db generation
SeqIO is has no desc attribute