From 3d030879dcfa11d464fe488950f41c1ed443be09 Mon Sep 17 00:00:00 2001 From: ChrisgKent Date: Wed, 1 Nov 2023 13:11:37 +0000 Subject: [PATCH 1/3] Auto updating index --- index.json | 60 +++++++++++++++++++++++++++--------------------------- 1 file changed, 30 insertions(+), 30 deletions(-) diff --git a/index.json b/index.json index fbe842b..eaf1422 100644 --- a/index.json +++ b/index.json @@ -10,13 +10,13 @@ "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", "species": [ 10407 ], @@ -29,13 +29,13 @@ "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", "species": [ 10407 ], @@ -54,13 +54,13 @@ "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", "species": [ 2697049 ], @@ -75,13 +75,13 @@ "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", "species": [ 2697049 ], @@ -96,13 +96,13 @@ "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", "species": [ 2697049 ], @@ -115,13 +115,13 @@ "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", "species": [ 2697049 ], @@ -136,13 +136,13 @@ "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", "species": [ 2697049 ], @@ -155,13 +155,13 @@ "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", "species": [ 2697049 ], @@ -174,13 +174,13 @@ "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", "species": [ 2697049 ], @@ -194,13 +194,13 @@ "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", "species": [ 2697049 ], From 7a0e309927630b455f692b294c57111d7d45b1a9 Mon Sep 17 00:00:00 2001 From: ChrisKBio Date: Wed, 1 Nov 2023 13:59:01 +0000 Subject: [PATCH 2/3] Added schemename, schemeversion and ampliconsize to the index.json --- .github/workflows/build_index.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/build_index.py b/.github/workflows/build_index.py index be18e36..d22becb 100644 --- a/.github/workflows/build_index.py +++ b/.github/workflows/build_index.py @@ -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( From bc30c5186ca8dc51bde87cb14e0a8fbf53372118 Mon Sep 17 00:00:00 2001 From: ChrisgKent Date: Wed, 1 Nov 2023 13:59:15 +0000 Subject: [PATCH 3/3] Auto updating index --- index.json | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/index.json b/index.json index eaf1422..292ba35 100644 --- a/index.json +++ b/index.json @@ -5,6 +5,7 @@ "500": { "v1.0.0": { "algorithmversion": "primaldigest:1.1.2", + "ampliconsize": 500, "authors": [ "quick lab", "artic network" @@ -17,6 +18,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", "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 ], @@ -24,6 +27,7 @@ }, "v1.1.0": { "algorithmversion": "primaldigest:1.1.3", + "ampliconsize": 500, "authors": [ "quick lab", "artic network" @@ -36,6 +40,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", "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 ], @@ -47,6 +53,7 @@ "400": { "v1.0.0": { "algorithmversion": "primalscheme1:1.0.0", + "ampliconsize": 400, "authors": [ "quick lab", "artic network" @@ -61,6 +68,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "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 ], @@ -68,6 +77,7 @@ }, "v2.0.0": { "algorithmversion": "primalscheme1:1.0.0", + "ampliconsize": 400, "authors": [ "quick lab", "artic network" @@ -82,6 +92,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "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 ], @@ -89,6 +101,7 @@ }, "v3.0.0": { "algorithmversion": "primalscheme1:1.0.0", + "ampliconsize": 400, "authors": [ "artic network", "quick lab" @@ -103,6 +116,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "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 ], @@ -110,6 +125,7 @@ }, "v4.0.0": { "algorithmversion": "primalscheme1:1.0.0", + "ampliconsize": 400, "authors": [ "quick lab", "artic network" @@ -122,6 +138,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "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 ], @@ -129,6 +147,7 @@ }, "v4.1.0": { "algorithmversion": "primalscheme1:1.0.0", + "ampliconsize": 400, "authors": [ "quick lab", "artic network" @@ -143,6 +162,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "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 ], @@ -150,6 +171,7 @@ }, "v5.0.0": { "algorithmversion": "primalscheme2:1.0.0", + "ampliconsize": 400, "authors": [ "quick lab", "artic network" @@ -162,6 +184,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "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 ], @@ -169,6 +193,7 @@ }, "v5.2.0": { "algorithmversion": "primalscheme2:1.0.0", + "ampliconsize": 400, "authors": [ "artic network", "quick lab" @@ -181,6 +206,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "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 ], @@ -188,6 +215,7 @@ }, "v5.3.2": { "algorithmversion": "primalscheme2:1.0.0", + "ampliconsize": 400, "authors": [ "artic network", "quick lab", @@ -201,6 +229,8 @@ "primerclass": "primerschemes", "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "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 ],