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Merge pull request #7 from ChrisgKent/main
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Updated index.json to contain scheme name, scheme version and ampliconsize
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@ChrisgKent
ChrisgKent authored Nov 2, 2023
2 parents 077833d + bc30c51 commit 847df81
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Showing 2 changed files with 64 additions and 30 deletions.
4 changes: 4 additions & 0 deletions .github/workflows/build_index.py
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,11 @@ def parse_version(
version_dict["species"] = info_dict["species"]
version_dict["license"] = info_dict["license"]
version_dict["primerclass"] = info_dict["primerclass"]
version_dict["schemename"] = info_dict["schemename"]
version_dict["schemeversion"] = info_dict["schemeversion"]
version_dict["ampliconsize"] = info_dict["ampliconsize"]


# Add the primer.bed file
primerbed = version_path / "primer.bed"
version_dict["primer_bed_url"] = create_rawlink(
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90 changes: 60 additions & 30 deletions index.json
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Original file line number Diff line number Diff line change
Expand Up @@ -5,37 +5,43 @@
"500": {
"v1.0.0": {
"algorithmversion": "primaldigest:1.1.2",
"ampliconsize": 500,
"authors": [
"quick lab",
"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": [
10407
],
"status": "draft"
},
"v1.1.0": {
"algorithmversion": "primaldigest:1.1.3",
"ampliconsize": 500,
"authors": [
"quick lab",
"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": [
10407
],
Expand All @@ -47,160 +53,184 @@
"400": {
"v1.0.0": {
"algorithmversion": "primalscheme1:1.0.0",
"ampliconsize": 400,
"authors": [
"quick lab",
"artic network"
],
"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": [
2697049
],
"status": "deprecated"
},
"v2.0.0": {
"algorithmversion": "primalscheme1:1.0.0",
"ampliconsize": 400,
"authors": [
"quick lab",
"artic network"
],
"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": [
2697049
],
"status": "deprecated"
},
"v3.0.0": {
"algorithmversion": "primalscheme1:1.0.0",
"ampliconsize": 400,
"authors": [
"artic network",
"quick lab"
],
"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": [
2697049
],
"status": "deprecated"
},
"v4.0.0": {
"algorithmversion": "primalscheme1:1.0.0",
"ampliconsize": 400,
"authors": [
"quick lab",
"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": [
2697049
],
"status": "deprecated"
},
"v4.1.0": {
"algorithmversion": "primalscheme1:1.0.0",
"ampliconsize": 400,
"authors": [
"quick lab",
"artic network"
],
"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": [
2697049
],
"status": "deprecated"
},
"v5.0.0": {
"algorithmversion": "primalscheme2:1.0.0",
"ampliconsize": 400,
"authors": [
"quick lab",
"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": [
2697049
],
"status": "deprecated"
},
"v5.2.0": {
"algorithmversion": "primalscheme2:1.0.0",
"ampliconsize": 400,
"authors": [
"artic network",
"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": [
2697049
],
"status": "deprecated"
},
"v5.3.2": {
"algorithmversion": "primalscheme2:1.0.0",
"ampliconsize": 400,
"authors": [
"artic network",
"quick lab",
"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": [
2697049
],
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