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superphy / spfy

Spfy: an integrated graph database for real-time prediction of Escherichia coli phenotypes and downstream comparative analyses
https://lfz.corefacility.ca/superphy/grouch/
Apache License 2.0
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More descriptive VF results #322

Closed kevinkle closed 6 years ago

kevinkle commented 6 years ago

We can probably do the same thing as with AMR results, hitname as currently, longname as the full string eg. putative adhesin [EaeH (CVF679)] [Escherichia coli O17:K52:H18 str. UMN026] then description as a link to https://www.ncbi.nlm.nih.gov/protein/ + the gi from our vf file. Would require modifications to our old branch of ectyper and a bit on spfy’s part to handle it

kevinkle commented 6 years ago

Two gi formats in our ref file. gnl|BL_ORD_ID|2624 SPG000066 (suba) Subtilase cytotoxin, subunit A, variant 1, Toxin, [gi|73853177:151027-152070 Escherichia coli EH41 plasmid pO113, complete sequence]

gnl|BL_ORD_ID|129 VFG000929(gi:26246560) (entD) phosphopantetheinyl transferase component of enterobactin synthase multienzyme complex [Enterobactin (VF0228)] [Escherichia coli CFT073]

and some with gb: gnl|BL_ORD_ID|2602 SPG000044 (espR2) gb|AIFJ01000038.1|:95193-96449 Escherichia coli DEC3F gecDEC3F.contig.37_1, whole genome shotgun sequence, leucine Rich Repeat family protein

and some without gi: gnl|BL_ORD_ID|2695 SPG000138 (ccdb) Plasmid KIL19 (from E.coli) cytotoxic protein (ccdB) gene, complete cds. [L27082 1-381]

kevinkle commented 6 years ago

Closing as of https://github.com/superphy/spfy/pull/323