feat: add influenza-a diamond db

Author: anna-parker

README.md

@@ -12,18 +12,18 @@ Then create a config.yaml file (like the example) with the list of all INSDC ref
 
 ```yaml
 references:
-  seg4_H1: U08903.1
-  seg4_H2: CY005413.1
-  seg3__H5N1: NC_007359.1
+  seg4-H1: U08903.1
+  seg4-H2: CY005413.1
+  seg3--H5N1: NC_007359.1
 ```
 
-Note that the key e.g. `seg4_H1` will be the prefix of the `dataset` name that is returned in the diamond blastx results.tsv. (As DIAMOND matches proteins each CDS in the sequence receives its own identifier, in Loculus we map all sequences that match the protein `id|CDS{i}` to the sequence `id`. ). The keys should be the same as your sequenceName they are assigned to e.g. `{segment}-{reference}` or alternatively, you can add lists of accepted matches to the `config.accepted_dataset_matches` field.
+Note that the key e.g. `seg4-H1` will be the prefix of the `dataset` name that is returned in the diamond blastx results.tsv. (As DIAMOND matches proteins each CDS in the sequence receives its own identifier, in Loculus we map all sequences that match the protein `id|CDS{i}` to the sequence `id`. ). The keys should be the same as your sequenceName they are assigned to e.g. `{segment}-{reference}` or alternatively, you can add lists of accepted matches to the `config.accepted_dataset_matches` field.
 
 ```tsv
 seqName	dataset	pident	...
-MW874350.1	seg3__H5N1|CDS1	0.4829120176662018	...
-MW874350.1	seg3__H1N1|CDS2	0.34937439846005774	...
-MW874350.1	seg3__H3N2|CDS1	0.22552301255230126	...
+MW874350.1	seg3-H5N1|CDS1	0.4829120176662018	...
+MW874350.1	seg3-H1N1|CDS2	0.34937439846005774	...
+MW874350.1	seg3-H3N2|CDS1	0.22552301255230126	...
 ```
 
 ```bash 

results/influenza-a/config.yaml

@@ -0,0 +1,58 @@
+references:
+  seg1-h1n1pdm: NC_002205.1
+  seg1-h1n1: NC_002023.1
+  seg1-h3n2: NC_007373.1
+  seg1-h2n2: NC_007378.1
+  seg2-h1n1pdm: NC_026435.1
+  seg2-h1n1: NC_002021.1
+  seg2-h3n2: NC_007372.1
+  seg2-h2n2: NC_007375.1
+  seg3-h1n1pdm: NC_026437.1
+  seg3-h1n1: NC_002022.1
+  seg3-h3n2: NC_007371.1
+  seg3-h2n2: NC_007376.1
+  seg4-h3_h3n8: CY028836
+  seg4-h4_h4n6: CY181241
+  seg4-h5_h5n1: NC_007362.1
+  seg4-h5_h5n2: KU143256
+  seg4-h6_h6n2: CY130030
+  seg4-h7_h7n9: NC_026425.1
+  seg4-h8_h8n4: CY136131
+  seg4-h9_h9n2: NC_004908.1
+  seg4-h10_h10n7: CY136094
+  seg4-h11_h11n9: CY130070
+  seg4-h12_h12n5: CY130078
+  seg4-h13_h13n6: CY130086
+  seg4-h14_h14n5: JN696314
+  seg4-h15_h15n9: CY006010
+  seg4-h16_h16n3: CY136630
+  seg4-h17_h17n10: CY103876
+  seg4-h18_h18n11: CY125945
+  seg5-h1n1pdm: NC_026436.1
+  seg5-h1n1: NC_002019.1
+  seg5-h3n2: NC_007369.1
+  seg5-h2n2: NC_007378.1
+  seg6-n1_h5n1: NC_007361.1
+  seg6-n2_h6n2: CY130032
+  seg6-n2_h9n2: NC_004909.1
+  seg6-n2_h5n2: KU143347
+  seg6-n3_h16n3: CY136632
+  seg6-n4_h8n4: CY136133
+  seg6-n5_h12n5: CY130080
+  seg6-n6_h4n6: CY181243
+  seg6-n6_h13n6: CY130088
+  seg6-n7_h10n7: CY136096
+  seg6-n8_h3n8: CY028838
+  seg6-n9_h7n9: NC_026429.1
+  seg6-n9_h11n9: CY130072
+  seg6-n9_h15n9: CY005407
+  seg6-n10_h17n10: CY103878
+  seg6-n11_h18n11: CY125947
+  seg7-h1n1pdm: NC_026431.1
+  seg7-h1n1: NC_002016.1
+  seg7-h3n2: NC_007367.1
+  seg7-h2n2: NC_007377.1
+  seg8-h1n1pdm: NC_026432.1
+  seg8-h1n1: NC_002020.1
+  seg8-h3n2: NC_007370.1
+  seg8-h2n2: NC_007380.1