Dev (#3)

* new locus definitions

* STEC schemes and scheme table updates

* doc for STEC loci

* github action to check for database files

* fix dir for check

* m

* m

* added salm org settings

* check optional files

.github/workflows/check-dbs.yml

@@ -0,0 +1,25 @@
+# make a workflow called check-dbs
+name: check-dbs
+on: [push]
+
+jobs:
+  check-dbs:
+    strategy:
+      matrix:
+        db: [CAMPY, CBOT, CRONO, LISTERIA, SALM, STEC, VIBR]
+    runs-on: ubuntu-20.04
+    steps:
+    - uses: actions/checkout@v4
+    - name: Check mandatory files
+      run: |
+        set -x
+        ls db/${{ matrix.db }}/alleles_0.*
+        ls db/${{ matrix.db }}/alleleinfo.txt_0
+        ls db/${{ matrix.db }}/loci.tsv
+        ls db/${{ matrix.db }}/OrganismSettings.json
+    - name: Check optional files
+      run: |
+        set -x
+        ls db/${{ matrix.db }}/alleles.fasta.gz || true
+        ls -a db/${{ matrix.db }}/loci || true
+        

README.md

@@ -4,15 +4,15 @@ These are databases for use with the PN2.0 caller.
 
 ## Databases
 
-| scheme   | directory |
-| ------   | --------- |
-| _Campylobacter_ | [db/CAMPY](/db/CAMPY/) |
-| _C. botulinum_  | [db/CBOT](/db/CBOT/) |
-| _Cronobacter_   | [db/CRONO](/db/CRONO/) |
-| _Listeria monocytogenes_ | [db/LISTERIA](/db/LISTERIA/) |
-| _Salmonella enterica_    | [db/SALM](/db/SALM/) |
-| Shiga toxin producing _E. coli_ | [db/STEC](/db/STEC/) |
-| _Vibrio_        | [db/VIBR](/db/VIBR/) |
+| scheme   | target | directory |
+| ------   | ------ | --------- |
+| _Campylobacter_ | _C. jejuni_, _C. coli_,  | [db/CAMPY](/db/CAMPY/) |
+| _C. botulinum_  | _C. botulinum_           | [db/CBOT](/db/CBOT/) |
+| _Cronobacter_   | _Cronobacter_ spp.       | [db/CRONO](/db/CRONO/) |
+| _Listeria_      | _Listeria monocytogenes_ | [db/LISTERIA](/db/LISTERIA/) |
+| _Salmonella_    | _Salmonella_ spp.        | [db/SALM](/db/SALM/) |
+| STEC            | _Escherichia_, especially Shiga toxin producing _E. coli_ or _Shigella_ | [db/STEC](/db/STEC/) |
+| _Vibrio_        | _V. cholerae_, _V. vulnificus_, and _V. parahaemolyticus_ | [db/VIBR](/db/VIBR/) |
 
 ## Database structure
 
@@ -25,6 +25,7 @@ More details for the files are given in subsections below the table.
 | alleles_0.* | The blast database |
 | aleleleinfo.txt_0 | A four-column file describing each allele |
 | loci.tsv | A two column file describing each locus |
+| loci/    | (optional) A directory of alternative locus labels. In the case of _Vibrio_, it shows different labels per organism. |
 | OrganismSettings.json | Description of custom settings per schema |
 
 ### alleleinfo.txt_0