Starting optimizing protein grouping by less trips to db. 1 - test master db generation
Merge branch 'master' into faster_protein_grouping
Typos
Restructured sqlite lookup table for protein-peptide lookups
Foreign keys for psm_protein_groups to both master and psm id
Some interface changes peptides -> psms and new master storing code for faster processing
Build master db from psms
Fetch protein group content from masters
Store protein group content
Store more protein information such as pep and psm count in db
MSGFScore is an integer, not float
Added empty init for dataformats module
Changed a docstring
Changed sort functions to sort info from db records by key
Lookup all protein group content from sqlite before it is sorted in a big join
Switched psm / protpepmap fetching to multi table join
More than one (temporary) master may be found in a protein group if they share all peptides. We will sort later
Index of database records of a protein group return should be constants
Sorting protein groups gets function call and counting protein hits in group too.
Removing some crap, fixing a docstring, and adding function arguments