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erikrikarddaniel / pfitmap

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Create released_db model and refer to it from protein_count, protein and taxon #77

Closed erikrikarddaniel closed 10 years ago

erikrikarddaniel commented 10 years ago

Remove references from protein_count, protein and taxon to pfitmap_release and sequence_database. Replace with reference to new model: released_db (see DIA model; references to pfitmap_release and load_database).

binnisb commented 10 years ago

Now the protein counts has a column in the database for sequence source. That should not be there, right? That goes together with pfitmap release.

binnisb commented 10 years ago

Protein: (id: integer, hmm_profile_id: integer, created_at: datetime, updated_at: datetime, protclass: string, subclass: string, group: string, subgroup: string, subsubgroup: string, protfamily: string)

I can remove the hmm_profile_id column from Protein as well right? Now it is used in the proteins initialize_protein function. That function loops over all HmmProfiles and generates all proteins from that. This functionality should be in the pfitmap_release.calculate function rather than on proteins?

binnisb commented 10 years ago

I can remove the obs_as_genome from ProteinCount right?

binnisb commented 10 years ago

I should not remove the wgs from Taxon right?

erikrikarddaniel commented 10 years ago

2013/10/25 Brynjar Smári Bjarnason notifications@github.com

Now the protein counts has a column in the database for sequence source. That should not be there, right? That goes together with pfitmap release.

No, it shouldn't be there, it's replaced with a reference to the released_database model. /D

— Reply to this email directly or view it on GitHubhttps://github.com/erikrikarddaniel/pfitmap/issues/77#issuecomment-27072697 .