Merge pull request #17 from ChrisgKent/main

merge
quick-lab · Jan 18, 2024 · d8ac726 · d8ac726
2 parents a6b77b5 + 22b859e
commit d8ac726
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diff --git a/.github/workflows/build_index.yml b/.github/workflows/build_index.yml
@@ -19,6 +19,9 @@ jobs:
     steps:
     # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
     - uses: actions/checkout@v3
+    - uses: actions/setup-python@v4
+      with:
+        python-version: "3.11"
 
     # Runs commands using the runners shell
     - name: Run the build index script

diff --git a/index.json b/index.json
diff --git a/primerschemes/artic-pan-ebola/1000/v1.0.0/README.md b/primerschemes/artic-pan-ebola/1000/v1.0.0/README.md
@@ -0,0 +1,41 @@
+# artic-pan-ebola 1000bp v1.0.0
+
+## Overviews
+
+![NC_006432.1.png](work/NC_006432.1.png)
+
+## Details
+
+```json
+{
+    "ampliconsize": 1000,
+    "schemeversion": "v1.0.0",
+    "schemename": "artic-pan-ebola",
+    "primer_bed_md5": "c58ec3b4d07d24499106fed6501016a9",
+    "reference_fasta_md5": "083c89a1798778fbe94a643d83a6fbb1",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "quick-lab",
+        "artic"
+    ],
+    "algorithmversion": "primalscheme3:1.1.0",
+    "species": [
+        3044781
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v1.1.0",
+    "articbedversion": "v3.0",
+    "description": null,
+    "derivedfrom": null
+}
+```
+
+
+
+------------------------------------------------------------------------
+
+This work is licensed under a [Creative Commons Attribution-ShareAlike 4.0 International License](http://creativecommons.org/licenses/by-sa/4.0/) 
+
+![](https://i.creativecommons.org/l/by-sa/4.0/88x31.png)
diff --git a/primerschemes/artic-pan-ebola/1000/v1.0.0/info.json b/primerschemes/artic-pan-ebola/1000/v1.0.0/info.json
@@ -0,0 +1,23 @@
+{
+    "ampliconsize": 1000,
+    "schemeversion": "v1.0.0",
+    "schemename": "artic-pan-ebola",
+    "primer_bed_md5": "c58ec3b4d07d24499106fed6501016a9",
+    "reference_fasta_md5": "083c89a1798778fbe94a643d83a6fbb1",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "quick-lab",
+        "artic"
+    ],
+    "algorithmversion": "primalscheme3:1.1.0",
+    "species": [
+        3044781
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v1.1.0",
+    "articbedversion": "v3.0",
+    "description": null,
+    "derivedfrom": null
+}
diff --git a/primerschemes/artic-pan-ebola/1000/v1.0.0/primer.bed b/primerschemes/artic-pan-ebola/1000/v1.0.0/primer.bed
@@ -0,0 +1,130 @@
+# artic-bed-version v3.0
+NC_006432.1	126	154	81307655_0_LEFT_0	1	+	CCTGGTTTATTTAACTAGTCAATCCCCC
+NC_006432.1	127	154	81307655_0_LEFT_1	1	+	CGATCCCCAATACCAACACTGAGAATT
+NC_006432.1	127	154	81307655_0_LEFT_2	1	+	GGAGACAATTTAACTAGTCAATCCCCC
+NC_006432.1	130	154	81307655_0_LEFT_3	1	+	GGTTTGTTTCAGAGCCACATCACA
+NC_006432.1	129	154	81307655_0_LEFT_4	1	+	TGGTTTGTTTCAGAGCCATATCACC
+NC_006432.1	1192	1222	81307655_0_RIGHT_0	1	-	GAGGATATGATCAAGCACTGTTTTGACTAT
+NC_006432.1	1192	1219	81307655_0_RIGHT_1	1	-	GATGTGGTCCAGAACAGTCTTTACAAT
+NC_006432.1	1192	1224	81307655_0_RIGHT_2	1	-	TGTAGGATATGATCAAGTACTGTTTTGACAAT
+NC_006432.1	1146	1169	81307655_1_LEFT_0	2	+	CGTCATTGCCAACTCTGTAGCTC
+NC_006432.1	1144	1169	81307655_1_LEFT_1	2	+	GCTGTGATTTCAAATTCAGTGGCTC
+NC_006432.1	1140	1169	81307655_1_LEFT_2	2	+	TGACACAGTAATATCTAATTCTGTTGCCC
+NC_006432.1	2219	2243	81307655_1_RIGHT_0	2	-	CGCTCTCAACATCTTCGTCACCTT
+NC_006432.1	2219	2243	81307655_1_RIGHT_1	2	-	CGTCCCTGTCCTGTTCTTCATCAT
+NC_006432.1	2219	2241	81307655_1_RIGHT_2	2	-	GTATCAGTGCTACCCTCGTCGT
+NC_006432.1	2219	2242	81307655_1_RIGHT_3	2	-	GTCCCTGTCCTGCTCTTCATCAT
+NC_006432.1	2219	2242	81307655_1_RIGHT_4	2	-	GTCCCTGTCCTGTTCTTCATCGT
+NC_006432.1	2124	2146	81307655_2_LEFT_0	1	+	GACCGCCAATCGAAGACTCTCA
+NC_006432.1	3196	3221	81307655_2_RIGHT_0	1	-	CGGAATCTTGCCTGTCATCAATTGC
+NC_006432.1	3196	3221	81307655_2_RIGHT_1	1	-	CGGTATTTTGCCGGTCATTAATTGC
+NC_006432.1	3196	3219	81307655_2_RIGHT_2	1	-	GAATCCTTCCGGTCATTAGCTGC
+NC_006432.1	3196	3220	81307655_2_RIGHT_3	1	-	GGAATTCTTCCGGTCATTAGCTGC
+NC_006432.1	3141	3162	81307655_3_LEFT_0	2	+	CAACAACCACAGGCACACGAT
+NC_006432.1	3135	3162	81307655_3_LEFT_1	2	+	CCATGCAGCAGGATAGGACTTATAGAC
+NC_006432.1	3138	3162	81307655_3_LEFT_2	2	+	CGGTCACGACTCAAAACGACAGAA
+NC_006432.1	3140	3162	81307655_3_LEFT_3	2	+	GCCACGACTCAAAACGACAGAA
+NC_006432.1	3140	3162	81307655_3_LEFT_4	2	+	GCCACGACTCAGAACGACAGAA
+NC_006432.1	4208	4237	81307655_3_RIGHT_0	2	-	GCTGCTAGCGAGATAAGAACAATTTTATC
+NC_006432.1	4208	4237	81307655_3_RIGHT_1	2	-	GCTGCTAGCGAGATATGAACAATTTTATC
+NC_006432.1	4208	4237	81307655_3_RIGHT_2	2	-	GCTGCTAGCGGGATATGAACAATTTTATC
+NC_006432.1	4208	4244	81307655_3_RIGHT_3	2	-	GGGAAATTTAAAACTGACTTATAAGCTTATGACATG
+NC_006432.1	4208	4241	81307655_3_RIGHT_4	2	-	GTTATTTTATTCTTAACAGTAGGTTGCATTGGA
+NC_006432.1	4067	4091	81307655_4_LEFT_0	1	+	AGGGGTTGGGTATGCATATTCCAG
+NC_006432.1	4063	4091	81307655_4_LEFT_1	1	+	CGATAGAGGTTGGGTCTGTATTTTTCAA
+NC_006432.1	4066	4091	81307655_4_LEFT_2	1	+	TCGAGGTTGGGTATGTGTTTTTCAG
+NC_006432.1	5163	5189	81307655_4_RIGHT_0	1	-	CCTGGAGTGAAGTCATTATTGCTTGG
+NC_006432.1	5163	5192	81307655_4_RIGHT_1	1	-	GGTCTTGGAGAAAGTTCATTATTGCTTGT
+NC_006432.1	5163	5188	81307655_4_RIGHT_2	1	-	TTGCATCAGGTTCACAATTGTCTGA
+NC_006432.1	5071	5097	81307655_5_LEFT_0	2	+	ATTTCATTTCATCCAAAACTTCGCCC
+NC_006432.1	5071	5097	81307655_5_LEFT_1	2	+	ATTTCCTTTCATCCCAAACTGAGACC
+NC_006432.1	5073	5097	81307655_5_LEFT_2	2	+	TTCATTTCACCCAAAGCTGAGACC
+NC_006432.1	6168	6197	81307655_5_RIGHT_0	2	-	CCAACTGATCTCAATTGATTTGTGGATGA
+NC_006432.1	6168	6192	81307655_5_RIGHT_1	2	-	CGATTTCAGCTGACTTGTGGAGGA
+NC_006432.1	6168	6193	81307655_5_RIGHT_2	2	-	CTGATTTCAGCTGGTCAGTAGATGC
+NC_006432.1	6168	6198	81307655_5_RIGHT_3	2	-	TCCAACTGATCTCAATTGATTTGTAGATGA
+NC_006432.1	6102	6134	81307655_6_LEFT_0	1	+	GGAGTTATCCACAATAGTACATTACAGGTTAG
+NC_006432.1	6108	6134	81307655_6_LEFT_1	1	+	GTTCACAACAACACTCTCCAGGTAAG
+NC_006432.1	6106	6134	81307655_6_LEFT_2	1	+	TCATCCACAATAGCACATTACAGGTTAG
+NC_006432.1	6104	6134	81307655_6_LEFT_3	1	+	TGTTGTGACTAACAGCACTTTAGAAGTAAC
+NC_006432.1	7179	7202	81307655_6_RIGHT_0	1	-	CCCGATGGTGGAGATCTGCATAT
+NC_006432.1	7179	7206	81307655_6_RIGHT_1	1	-	CCTCAGAGATGTCAAGTTTATACACGG
+NC_006432.1	7045	7068	81307655_7_LEFT_0	2	+	GGTTCAAGTGCACAGTCAAGGAA
+NC_006432.1	7046	7068	81307655_7_LEFT_1	2	+	GTTCAAGTGCGAGACCTCCAGA
+NC_006432.1	7044	7068	81307655_7_LEFT_2	2	+	TGGTTCCATTGCACATACCAGAAG
+NC_006432.1	8144	8174	81307655_7_RIGHT_0	2	-	AGCATTCCAGTTCAAAGGATTTTTGTAAAC
+NC_006432.1	8144	8179	81307655_7_RIGHT_1	2	-	CTCCAGTGTATTATATTGTCATTTGTCAAGTAATC
+NC_006432.1	8144	8179	81307655_7_RIGHT_2	2	-	CTCCAGTGTATTATGTTATCATTTGTCAAGTAATC
+NC_006432.1	8144	8180	81307655_7_RIGHT_3	2	-	GCTCCAGTGTATTATATTATCATTTGTCAAGTAATC
+NC_006432.1	7916	7940	81307655_8_LEFT_0	1	+	AATGACAATTGGTGGACAGGATGG
+NC_006432.1	7918	7940	81307655_8_LEFT_1	1	+	TGACAATTGGTGGACAGGGTGG
+NC_006432.1	7918	7940	81307655_8_LEFT_2	1	+	TGATAATTGGTGGACGGGCTGG
+NC_006432.1	8989	9012	81307655_8_RIGHT_0	1	-	TCACACAAAAGACTCAGCTGGGA
+NC_006432.1	8989	9014	81307655_8_RIGHT_1	1	-	TCTCACATAAAAGACTCAGCTGGGA
+NC_006432.1	8989	9018	81307655_8_RIGHT_2	1	-	TGACTCTCACATAATTGACTAAGCTGTGA
+NC_006432.1	8925	8954	81307655_9_LEFT_0	2	+	AGAGGATTCAAAGTTAAGAGCATTGTTGA
+NC_006432.1	8925	8954	81307655_9_LEFT_1	2	+	AGAGGATTCCAAATTAAGGGCATTGTTAA
+NC_006432.1	8922	8954	81307655_9_LEFT_2	2	+	CATAGAGGATTCAAAATTAAGAGCATTGTTGA
+NC_006432.1	8931	8954	81307655_9_LEFT_3	2	+	TGCAAAACTCCGTGCTCTCTTGA
+NC_006432.1	10014	10043	81307655_9_RIGHT_0	2	-	ATGTGTACAGACCAATTTAGCTTAGAGAC
+NC_006432.1	10014	10044	81307655_9_RIGHT_1	2	-	GGGATTCTGCGAGTAGACTAGTTCAATAAA
+NC_006432.1	10014	10040	81307655_9_RIGHT_2	2	-	TGTACAGACCACTTTAGCTCAGAGAC
+NC_006432.1	9872	9896	81307655_10_LEFT_0	1	+	CCCCAAGAGGCATTCTTCATCTCC
+NC_006432.1	9872	9896	81307655_10_LEFT_1	1	+	CCCCTAGAGGCATTCTTCATCTCC
+NC_006432.1	9871	9896	81307655_10_LEFT_2	1	+	CCTTGCTCTGCCAATTTTCATCTCC
+NC_006432.1	9866	9896	81307655_10_LEFT_3	1	+	GTTAGACTCTGTTCAAGGATCTTCATCTTT
+NC_006432.1	10966	10991	81307655_10_RIGHT_0	1	-	GGCAACAGGTTTAAGTGTCGATTCA
+NC_006432.1	10966	10992	81307655_10_RIGHT_1	1	-	GTGTAAATGCTTTCAGTGTGGACTCA
+NC_006432.1	10966	10994	81307655_10_RIGHT_2	1	-	TTTGATTAGAGCCTTGAAGGTTGATTCA
+NC_006432.1	10874	10897	81307655_11_LEFT_0	2	+	ACCAACATGGGTTTCCTGGTAGA
+NC_006432.1	10869	10897	81307655_11_LEFT_1	2	+	CCAGGACTAATATGGGTTATCTTGTCGA
+NC_006432.1	10871	10897	81307655_11_LEFT_2	2	+	CGAACTAACATGGGTTTTCTGGTGGA
+NC_006432.1	11900	11925	81307655_11_RIGHT_0	2	-	CATCAACACAGTCTTCTTGAGCACC
+NC_006432.1	11900	11930	81307655_11_RIGHT_1	2	-	TTGATCTGTAATTACTCCTTCCTGTGTTTT
+NC_006432.1	11814	11839	81307655_12_LEFT_0	1	+	AACCAAAGTGCAGCCAATTCTTAGA
+NC_006432.1	11816	11839	81307655_12_LEFT_1	1	+	CCTCCCTGCTTGAGTTTCTTGGA
+NC_006432.1	11817	11839	81307655_12_LEFT_2	1	+	CGCGGTGCCAACAGTTCTTAGA
+NC_006432.1	12880	12906	81307655_12_RIGHT_0	1	-	GATCTTTGATCATTGGAAGTGGAGGG
+NC_006432.1	12880	12904	81307655_12_RIGHT_1	1	-	TCTTTAATCATAGGCAGTGGCGGA
+NC_006432.1	12880	12904	81307655_12_RIGHT_2	1	-	TCTTTAATCATTGGCAACGGAGGG
+NC_006432.1	12816	12845	81307655_13_LEFT_0	2	+	ACAGTGTTACCTCAGATAGAAATCTCACA
+NC_006432.1	12818	12845	81307655_13_LEFT_1	2	+	AGTGTGATATCAGACCGATGTTTAACG
+NC_006432.1	12810	12845	81307655_13_LEFT_2	2	+	CATGGTATAGTGTAATCTCAGATAAACATCTAACA
+NC_006432.1	12813	12845	81307655_13_LEFT_3	2	+	GGTACAATGTTACTTCAGATAGGAATCTAACA
+NC_006432.1	12813	12845	81307655_13_LEFT_4	2	+	GGTACAGTGTTACCTCAGATAGAAATCTAACA
+NC_006432.1	12813	12845	81307655_13_LEFT_5	2	+	GGTACAGTGTTACTTCAGATAGGAATCTAACA
+NC_006432.1	13882	13908	81307655_13_RIGHT_0	2	-	CATCTGGTTTTAGGAAGATGCCACAG
+NC_006432.1	13882	13906	81307655_13_RIGHT_1	2	-	TCAGGCTTGAGGAATATCCCACAG
+NC_006432.1	13882	13913	81307655_13_RIGHT_2	2	-	TGTTTCATCAGGTTTTAAAAAGATTCCACAG
+NC_006432.1	13767	13795	81307655_14_LEFT_0	1	+	AGTGCATTACTGTTTTATCAGTCTTCCC
+NC_006432.1	13759	13795	81307655_14_LEFT_1	1	+	GGATAATCAATGTATTACAGTATTATCAGTCTTTCC
+NC_006432.1	13769	13795	81307655_14_LEFT_2	1	+	TGCATTACCGTTTTATCAGTCTTCCC
+NC_006432.1	14846	14879	81307655_14_RIGHT_0	1	-	TCTAAGAATTTGAGCAATATCAACAGTACACTT
+NC_006432.1	14846	14871	81307655_14_RIGHT_1	1	-	TCTGTGCTAAATCAACTGTGCAAGT
+NC_006432.1	14846	14870	81307655_14_RIGHT_2	1	-	TTGCGCCAAATCAACTGTACAAGA
+NC_006432.1	14799	14825	81307655_15_LEFT_0	2	+	ACCTAGACCACTGTGATCAGGTTCTA
+NC_006432.1	14800	14825	81307655_15_LEFT_1	2	+	CCTAGACCATTGTGACCCAGCTTTA
+NC_006432.1	14790	14825	81307655_15_LEFT_2	2	+	GGTTTAGTTATCTTGATCATTGTGATAATATCCTG
+NC_006432.1	15864	15886	81307655_15_RIGHT_0	2	-	AAGGATCTTGTTTCACCGCTGC
+NC_006432.1	15864	15890	81307655_15_RIGHT_1	2	-	AGTGAATGATCTTGTTTCTCCACTGC
+NC_006432.1	15864	15888	81307655_15_RIGHT_2	2	-	TGAATGATCGTGTTTCTCCACTGC
+NC_006432.1	15864	15888	81307655_15_RIGHT_3	2	-	TGAATGATCTTGTTTCTCCGCTGC
+NC_006432.1	15774	15796	81307655_16_LEFT_0	1	+	GGTTGCCACATTTATCCGGCTG
+NC_006432.1	15772	15796	81307655_16_LEFT_1	1	+	TCGACTGCCTCACTTATCTGGATG
+NC_006432.1	16872	16901	81307655_16_RIGHT_0	1	-	CCGTAAGTACTTTGATATCTCATCTTGGG
+NC_006432.1	16872	16900	81307655_16_RIGHT_1	1	-	CGTAAGTACTTTGATATCTCGTCTTGGG
+NC_006432.1	16872	16900	81307655_16_RIGHT_2	1	-	TGAAGTAACCCTTTTATATTACTGCGGC
+NC_006432.1	16793	16821	81307655_17_LEFT_0	2	+	ATCTCACATCGTCTAGTTCTACCTTTCT
+NC_006432.1	16797	16821	81307655_17_LEFT_1	2	+	CACACCGTCTAGTCCTACCTTTCT
+NC_006432.1	16795	16821	81307655_17_LEFT_2	2	+	CTCACATCGTCTAGTCCTACCTTTCT
+NC_006432.1	16795	16821	81307655_17_LEFT_3	2	+	TCCGCATCGTTTAGTAGTACCATTCT
+NC_006432.1	16795	16821	81307655_17_LEFT_4	2	+	TTCACACCGAATTGTCCTACCATTTT
+NC_006432.1	17887	17916	81307655_17_RIGHT_0	2	-	AATCATTCACTAGTTTAGTTATCCGTCCC
+NC_006432.1	17887	17915	81307655_17_RIGHT_1	2	-	ATCATTGACTAGTTTTGTGATTCGTCCT
+NC_006432.1	17887	17914	81307655_17_RIGHT_2	2	-	TCATTGACTAATTTTGTAATCCGGCCC
+NC_006432.1	17050	17078	81307655_18_LEFT_0	1	+	ACTACTGATCCAAAAATACGGCGTTAAG
+NC_006432.1	17045	17078	81307655_18_LEFT_1	1	+	GCCTTACTATTGATCCAGAAATACCAAGTTAAA
+NC_006432.1	17045	17078	81307655_18_LEFT_2	1	+	GCCTTACTATTGATTCAGAAATACCAAGTTAAG
+NC_006432.1	18096	18122	81307655_18_RIGHT_0	1	-	CCCTGTCAGCCTTTCAATAAGCTTAA
+NC_006432.1	18096	18122	81307655_18_RIGHT_1	1	-	CCCTGTCAGCCTTTCGATAAGCTTAA
+NC_006432.1	18096	18120	81307655_18_RIGHT_2	1	-	TGGTGAGCCGGTCCATAAGTTTTA