Merge pull request #8 from ChrisgKent/main

added the norovirus-gii scheme
quick-lab · Nov 3, 2023 · 3f11b29 · 3f11b29
2 parents 1a209c4 + 2ff835b
commit 3f11b29
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Showing 16 changed files with 362,584 additions and 32 deletions.
diff --git a/.github/workflows/build_index.py b/.github/workflows/build_index.py
@@ -60,11 +60,11 @@ def parse_version(
     # Check the hashes in the config.json file match the generated hashes
     if version_dict["primer_bed_md5"] != info_dict["primer_bed_md5"]:
         raise ValueError(
-            f"Hash mismatch for {version_dict['primer.bed.url']}. Expected {version_dict['primer_bed_md5']} but got {info_dict['primer_bed_md5']}"
+            f"Hash mismatch for {version_dict['primer_bed_md5']}. Expected {version_dict['primer_bed_md5']} but got {info_dict['primer_bed_md5']}"
         )
     if version_dict["reference_fasta_md5"] != info_dict["reference_fasta_md5"]:
         raise ValueError(
-            f"Hash mismatch for {version_dict['reference.fasta.url']}. Expected {version_dict['reference_fasta_md5']} but got {info_dict['reference_fasta_md5']}"
+            f"Hash mismatch for {version_dict['reference_fasta_md5']}. Expected {version_dict['reference_fasta_md5']} but got {info_dict['reference_fasta_md5']}"
         )
 
     return version_dict

diff --git a/index.json b/index.json
@@ -11,13 +11,13 @@
                         "artic network"
                     ],
                     "citations": [],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/hbv/500/v1.0.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "f1874f2b2332dff4b4cd6f0075f128dd",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/hbv/500/v1.0.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7612eab3e2389215206ae17187da1791",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/hbv/500/v1.0.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/reference.fasta",
                     "schemename": "hbv",
                     "schemeversion": "v1.0.0",
                     "species": [
@@ -33,13 +33,13 @@
                         "artic network"
                     ],
                     "citations": [],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/hbv/500/v1.1.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.1.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "dd96ade2e5c59377808368cc116a8361",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/hbv/500/v1.1.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.1.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7612eab3e2389215206ae17187da1791",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/hbv/500/v1.1.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.1.0/reference.fasta",
                     "schemename": "hbv",
                     "schemeversion": "v1.1.0",
                     "species": [
@@ -49,6 +49,32 @@
                 }
             }
         },
+        "norovirus-gii": {
+            "800": {
+                "v1.0.0": {
+                    "algorithmversion": "primaldigest:1.2.2",
+                    "ampliconsize": 800,
+                    "authors": [
+                        "quick lab",
+                        "artic network"
+                    ],
+                    "citations": [],
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/norovirus-gii/800/v1.0.0/info.json",
+                    "license": "CC BY-SA 4.0",
+                    "primer_bed_md5": "3191ec8a80f14a5688d561fe2cf77e34",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/norovirus-gii/800/v1.0.0/primer.bed",
+                    "primerclass": "primerschemes",
+                    "reference_fasta_md5": "88cba0415494cd9837e2523051cb636f",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/norovirus-gii/800/v1.0.0/reference.fasta",
+                    "schemename": "norovirus-gii",
+                    "schemeversion": "v1.0.0",
+                    "species": [
+                        122929
+                    ],
+                    "status": "draft"
+                }
+            }
+        },
         "sars-cov-2": {
             "400": {
                 "v1.0.0": {
@@ -61,13 +87,13 @@
                     "citations": [
                         "https://doi.org/10.1038/nprot.2017.066"
                     ],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "907d8d0e3efecd82e07120eda2b70d89",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/reference.fasta",
                     "schemename": "sars-cov-2",
                     "schemeversion": "v1.0.0",
                     "species": [
@@ -85,13 +111,13 @@
                     "citations": [
                         "https://doi.org/10.1038/nprot.2017.066"
                     ],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "c9916963e43951541e8a11274e0ac0df",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/reference.fasta",
                     "schemename": "sars-cov-2",
                     "schemeversion": "v2.0.0",
                     "species": [
@@ -109,13 +135,13 @@
                     "citations": [
                         "https://doi.org/10.1038/nprot.2017.066"
                     ],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "03e1c3eecc21bdb66a4bec990e0225cc",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/reference.fasta",
                     "schemename": "sars-cov-2",
                     "schemeversion": "v3.0.0",
                     "species": [
@@ -131,13 +157,13 @@
                         "artic network"
                     ],
                     "citations": [],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "6c42c61f304702adc6c550ad0941ed6f",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/reference.fasta",
                     "schemename": "sars-cov-2",
                     "schemeversion": "v4.0.0",
                     "species": [
@@ -155,13 +181,13 @@
                     "citations": [
                         "https://doi.org/10.1038/nprot.2017.066"
                     ],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/reference.fasta",
                     "schemename": "sars-cov-2",
                     "schemeversion": "v4.1.0",
                     "species": [
@@ -177,13 +203,13 @@
                         "artic network"
                     ],
                     "citations": [],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "6292814b0ec248605c72707d34dda1eb",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/reference.fasta",
                     "schemename": "sars-cov-2",
                     "schemeversion": "v5.0.0",
                     "species": [
@@ -199,13 +225,13 @@
                         "quick lab"
                     ],
                     "citations": [],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "6de462d8ffffcfb2aa37f7eeb205d94b",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/reference.fasta",
                     "schemename": "sars-cov-2",
                     "schemeversion": "v5.2.0",
                     "species": [
@@ -222,13 +248,13 @@
                         "bccdc"
                     ],
                     "citations": [],
-                    "info_json_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/info.json",
+                    "info_json_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/info.json",
                     "license": "CC-BY-4.0",
                     "primer_bed_md5": "722d56c381bf301aa9c5ae8721c78063",
-                    "primer_bed_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/primer.bed",
+                    "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/primer.bed",
                     "primerclass": "primerschemes",
                     "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c",
-                    "reference_fasta_url": "https://raw.githubusercontent.com/quick-lab/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/reference.fasta",
+                    "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/reference.fasta",
                     "schemename": "sars-cov-2",
                     "schemeversion": "v5.3.2",
                     "species": [

diff --git a/primerschemes/norovirus-gii/800/v1.0.0/README.md b/primerschemes/norovirus-gii/800/v1.0.0/README.md
@@ -0,0 +1,43 @@
+# norovirus-gii 800bp v1.0.0
+
+## Description
+
+A scheme designed for pan Norovirus gii
+
+## Overviews
+
+![NC_044932.1.png](work/NC_044932.1.png)
+
+## Details
+
+```json
+{
+    "ampliconsize": 800,
+    "schemeversion": "v1.0.0",
+    "schemename": "norovirus-gii",
+    "primer_bed_md5": "3191ec8a80f14a5688d561fe2cf77e34",
+    "reference_fasta_md5": "88cba0415494cd9837e2523051cb636f",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "quick lab",
+        "artic network"
+    ],
+    "algorithmversion": "primaldigest:1.2.2",
+    "species": [
+        122929
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v1.0.0",
+    "description": "A scheme designed for pan Norovirus gii"
+}
+```
+
+
+
+------------------------------------------------------------------------
+
+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/norovirus-gii/800/v1.0.0/info.json b/primerschemes/norovirus-gii/800/v1.0.0/info.json
@@ -0,0 +1,21 @@
+{
+    "ampliconsize": 800,
+    "schemeversion": "v1.0.0",
+    "schemename": "norovirus-gii",
+    "primer_bed_md5": "3191ec8a80f14a5688d561fe2cf77e34",
+    "reference_fasta_md5": "88cba0415494cd9837e2523051cb636f",
+    "status": "draft",
+    "citations": [],
+    "authors": [
+        "quick lab",
+        "artic network"
+    ],
+    "algorithmversion": "primaldigest:1.2.2",
+    "species": [
+        122929
+    ],
+    "license": "CC BY-SA 4.0",
+    "primerclass": "primerschemes",
+    "infoschema": "v1.0.0",
+    "description": "A scheme designed for pan Norovirus gii"
+}