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SEA-PHAGES / starterator

Released Stable version of Starterator for SEA phages; Note does not work with current version of phamerator database! For version compatible with current phamerator database, see this repo: cdshaffer/starterator
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switch determination of draft status to phage table field #21

Closed cdshaffer closed 6 years ago

cdshaffer commented 8 years ago

entries in field should be final or draft or GBK; may be some odd entries

cdshaffer commented 7 years ago

There are now new table entry AnnotationQC which can be used, this marks both phages that have passed QC and published by SEA-phages and other phage annotations which agree with the SEA-phages policies for ambigious gene calls:

  1. RetrieveRecord; TINYINT(1); default = 0
  2. AnnotationQC; TINYINT(1); default = 0

It doesn’t look like there is a BOOLEAN datatype, so I went with TINYINT(1) as we do with the cdd_status field. For now, I have set all ‘final’ status phages (819 total) to AnnotationQC = 1, and all ‘draft’ and ‘gbk’ phages remain at 0. So Chris, you are good to go to start using this field to weight different annotations in Starterator. As far as the RetrieveRecord field, I’ll wrap up the code this weekend to start implementing it. So from now on, all new ‘final’ annotation genomes added to the database will be set to be automatically updated from NCBI.

cdshaffer commented 6 years ago

new code which uses this field to determine status is in cdshaffer/starterator in the draft_status branch. This branch does correctly set the status however it does not change phageid or phage name.

I still thinking having some indication in the name of the phage as to its exact status might be preferable to having that not available. So this issue will remain open for the time being.

cdshaffer commented 6 years ago

policy has been decided to keep the using the name field with the _draft so that users know the status of the phage, but the determination of quality now uses the value in the phage.status field of the phamerator database. Starterator now considers only 'final' status as non_draft.