From c0d204a2bd3d3ff4452a41022b59939a3370d88f Mon Sep 17 00:00:00 2001 From: ChrisKent Date: Fri, 27 Oct 2023 16:57:20 +0100 Subject: [PATCH 1/2] Moved to v1.0.0 of the schema --- .github/workflows/build_index.py | 51 +++++------- README.md | 4 +- index.json | 80 +++++++++---------- primerschemes/hbv/500/v1.0.0/README.md | 32 ++++---- primerschemes/hbv/500/v1.0.0/info.json | 12 ++- primerschemes/hbv/500/v1.0.0/work/config.json | 2 +- primerschemes/hbv/500/v1.1.0/README.md | 32 ++++---- primerschemes/hbv/500/v1.1.0/info.json | 23 ++++-- primerschemes/hbv/500/v1.1.0/work/config.json | 4 +- primerschemes/sars-cov-2/400/v1.0.0/README.md | 34 ++++---- primerschemes/sars-cov-2/400/v1.0.0/info.json | 23 ++++-- .../sars-cov-2/400/v1.0.0/work/config.json | 4 +- primerschemes/sars-cov-2/400/v2.0.0/README.md | 34 ++++---- primerschemes/sars-cov-2/400/v2.0.0/info.json | 23 ++++-- .../sars-cov-2/400/v2.0.0/work/config.json | 4 +- primerschemes/sars-cov-2/400/v3.0.0/README.md | 38 +++++---- primerschemes/sars-cov-2/400/v3.0.0/info.json | 27 ++++--- .../sars-cov-2/400/v3.0.0/work/config.json | 4 +- primerschemes/sars-cov-2/400/v4.0.0/README.md | 32 ++++---- primerschemes/sars-cov-2/400/v4.0.0/info.json | 21 +++-- .../sars-cov-2/400/v4.0.0/work/config.json | 4 +- primerschemes/sars-cov-2/400/v4.1.0/README.md | 34 ++++---- primerschemes/sars-cov-2/400/v4.1.0/info.json | 23 ++++-- .../sars-cov-2/400/v4.1.0/work/config.json | 4 +- primerschemes/sars-cov-2/400/v5.0.0/README.md | 32 ++++---- primerschemes/sars-cov-2/400/v5.0.0/info.json | 21 +++-- .../sars-cov-2/400/v5.0.0/work/config.json | 4 +- primerschemes/sars-cov-2/400/v5.2.0/README.md | 36 +++++---- primerschemes/sars-cov-2/400/v5.2.0/info.json | 25 +++--- .../sars-cov-2/400/v5.2.0/work/config.json | 4 +- primerschemes/sars-cov-2/400/v5.3.2/README.md | 34 ++++---- primerschemes/sars-cov-2/400/v5.3.2/info.json | 23 ++++-- .../sars-cov-2/400/v5.3.2/work/config.json | 4 +- 33 files changed, 421 insertions(+), 311 deletions(-) diff --git a/.github/workflows/build_index.py b/.github/workflows/build_index.py index 7c9ae7e..be18e36 100644 --- a/.github/workflows/build_index.py +++ b/.github/workflows/build_index.py @@ -2,22 +2,6 @@ import json import sys import hashlib -from enum import Enum -import itertools - -""" -Version Schema - -requires an info.json in the version directory -{ - "ampliconsize": 100, - "schemeversion": "v1.0.0", - "schemename": "scheme_name", - "primer.bed.md5": "md5", - "reference.fasta.md5": "md5", -} - -""" def hashfile(fname): @@ -46,36 +30,37 @@ def parse_version( version_dict["status"] = info_dict["status"] version_dict["authors"] = info_dict["authors"] version_dict["citations"] = info_dict["citations"] + version_dict["species"] = info_dict["species"] + version_dict["license"] = info_dict["license"] + version_dict["primerclass"] = info_dict["primerclass"] # Add the primer.bed file primerbed = version_path / "primer.bed" - version_dict["primer.bed.url"] = create_rawlink( + version_dict["primer_bed_url"] = create_rawlink( repo_url, scheme_name, length, version.name, primerbed.name, pclass ) - version_dict["primer.bed.md5"] = hashfile(primerbed) + version_dict["primer_bed_md5"] = hashfile(primerbed) # Add the reference.fasta file reference = version_path / "reference.fasta" - version_dict["reference.fasta.url"] = create_rawlink( + version_dict["reference_fasta_url"] = create_rawlink( repo_url, scheme_name, length, version.name, reference.name, pclass ) - version_dict["reference.fasta.md5"] = hashfile(reference) + version_dict["reference_fasta_md5"] = hashfile(reference) - # Add the config.json file - config = version_path / "work/config.json" - version_dict["config.json.url"] = create_rawlink( - repo_url, scheme_name, length, version.name, "work/config.json", pclass + # Add the info.json file url + version_dict["info_json_url"] = create_rawlink( + repo_url, scheme_name, length, version.name, "info.json", pclass ) - version_dict["config.json.md5"] = hashfile(config) # Check the hashes in the config.json file match the generated hashes - if version_dict["primer.bed.md5"] != info_dict["primer.bed.md5"]: + 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.url']}. Expected {version_dict['primer_bed_md5']} but got {info_dict['primer_bed_md5']}" ) - if version_dict["reference.fasta.md5"] != info_dict["reference.fasta.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.url']}. Expected {version_dict['reference_fasta_md5']} but got {info_dict['reference_fasta_md5']}" ) return version_dict @@ -154,10 +139,10 @@ def check_consistency(existing_json, new_json): for path in intersection: # Check that the reference hashes are the same existing_ref_hash = existing_json[path[0]][path[1]][path[2]][path[3]][ - "reference.fasta.md5" + "reference_fasta_md5" ] new_ref_hash = new_json[path[0]][path[1]][path[2]][path[3]][ - "reference.fasta.md5" + "reference_fasta_md5" ] if existing_ref_hash != new_ref_hash: raise ValueError( @@ -166,9 +151,9 @@ def check_consistency(existing_json, new_json): # Check that the primer.bed hashes are the same existing_bed_hash = existing_json[path[0]][path[1]][path[2]][path[3]][ - "primer.bed.md5" + "primer_bed_md5" ] - new_bed_hash = new_json[path[0]][path[1]][path[2]][path[3]]["primer.bed.md5"] + new_bed_hash = new_json[path[0]][path[1]][path[2]][path[3]]["primer_bed_md5"] if existing_ref_hash != new_ref_hash: raise ValueError( f"Hash changed for {path[0]}/{path[1]}/{path[2]}/{path[3]}/primer.bed. Expected {existing_bed_hash} but got {new_bed_hash}" diff --git a/README.md b/README.md index 9b2ce84..7b0a9a5 100644 --- a/README.md +++ b/README.md @@ -77,8 +77,8 @@ primerschemes / primerpanels "ampliconsize": "int", "schemeversion": "str", "schemename": "str", -"primer.bed.md5": "str", -"reference.fasta.md5": "str", +"primer_bed_md5": "str", +"reference_fasta_md5": "str", "status": ["withdrawn", "deprecated", "autogenerated","draft","testing","validated"], "citations": "list[str]", "authors": "list[str]", diff --git a/index.json b/index.json index e8fd887..678a3c0 100644 --- a/index.json +++ b/index.json @@ -12,10 +12,10 @@ "citations": [], "config.json.md5": "4137d7ad6f0cc949be434fdb3480eef9", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/work/config.json", - "primer.bed.md5": "f1874f2b2332dff4b4cd6f0075f128dd", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/primer.bed", - "reference.fasta.md5": "7612eab3e2389215206ae17187da1791", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/reference.fasta", + "primer_bed_md5": "f1874f2b2332dff4b4cd6f0075f128dd", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/primer.bed", + "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/reference.fasta", "status": "draft" }, "v1.1.0": { @@ -27,10 +27,10 @@ "citations": [], "config.json.md5": "6c9ffb3f43cff3f19a484c58de623b2d", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.1.0/work/config.json", - "primer.bed.md5": "dd96ade2e5c59377808368cc116a8361", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.1.0/primer.bed", - "reference.fasta.md5": "7612eab3e2389215206ae17187da1791", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.1.0/reference.fasta", + "primer_bed_md5": "dd96ade2e5c59377808368cc116a8361", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.1.0/primer.bed", + "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.1.0/reference.fasta", "status": "draft" } } @@ -46,10 +46,10 @@ "citations": [], "config.json.md5": "8770bbec9c990777ba37e29ab3faaf24", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/work/config.json", - "primer.bed.md5": "907d8d0e3efecd82e07120eda2b70d89", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/primer.bed", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/reference.fasta", + "primer_bed_md5": "907d8d0e3efecd82e07120eda2b70d89", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/primer.bed", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v1.0.0/reference.fasta", "status": "deprecated" }, "v2.0.0": { @@ -61,10 +61,10 @@ "citations": [], "config.json.md5": "3ec0f600db89844c0740f3579878db0a", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/work/config.json", - "primer.bed.md5": "c9916963e43951541e8a11274e0ac0df", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/primer.bed", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/reference.fasta", + "primer_bed_md5": "c9916963e43951541e8a11274e0ac0df", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/primer.bed", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v2.0.0/reference.fasta", "status": "deprecated" }, "v3.0.0": { @@ -76,10 +76,10 @@ "citations": [], "config.json.md5": "65df78e6cddf16490e059c968ef6360b", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/work/config.json", - "primer.bed.md5": "03e1c3eecc21bdb66a4bec990e0225cc", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/primer.bed", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/reference.fasta", + "primer_bed_md5": "03e1c3eecc21bdb66a4bec990e0225cc", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/primer.bed", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v3.0.0/reference.fasta", "status": "deprecated" }, "v4.0.0": { @@ -91,10 +91,10 @@ "citations": [], "config.json.md5": "808f4d8539869329a3a0c6fedb059235", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/work/config.json", - "primer.bed.md5": "6c42c61f304702adc6c550ad0941ed6f", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/primer.bed", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/reference.fasta", + "primer_bed_md5": "6c42c61f304702adc6c550ad0941ed6f", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/primer.bed", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.0.0/reference.fasta", "status": "deprecated" }, "v4.1.0": { @@ -106,10 +106,10 @@ "citations": [], "config.json.md5": "467c9c6db43dd814090094113f46a979", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/work/config.json", - "primer.bed.md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/primer.bed", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/reference.fasta", + "primer_bed_md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/primer.bed", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v4.1.0/reference.fasta", "status": "deprecated" }, "v5.0.0": { @@ -121,10 +121,10 @@ "citations": [], "config.json.md5": "28512fe735517c6746f75396522cfe8b", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/work/config.json", - "primer.bed.md5": "6292814b0ec248605c72707d34dda1eb", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/primer.bed", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/reference.fasta", + "primer_bed_md5": "6292814b0ec248605c72707d34dda1eb", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/primer.bed", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.0.0/reference.fasta", "status": "deprecated" }, "v5.2.0": { @@ -136,10 +136,10 @@ "citations": [], "config.json.md5": "ba8e6c0af962ae492782c2c7025fe8f5", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/work/config.json", - "primer.bed.md5": "6de462d8ffffcfb2aa37f7eeb205d94b", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/primer.bed", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/reference.fasta", + "primer_bed_md5": "6de462d8ffffcfb2aa37f7eeb205d94b", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/primer.bed", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.2.0/reference.fasta", "status": "deprecated" }, "v5.3.2": { @@ -152,10 +152,10 @@ "citations": [], "config.json.md5": "fccf238204f6873bc83833ae345d877a", "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/work/config.json", - "primer.bed.md5": "722d56c381bf301aa9c5ae8721c78063", - "primer.bed.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/primer.bed", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "reference.fasta.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/reference.fasta", + "primer_bed_md5": "722d56c381bf301aa9c5ae8721c78063", + "primer_bed_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/primer.bed", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/sars-cov-2/400/v5.3.2/reference.fasta", "status": "validated" } } diff --git a/primerschemes/hbv/500/v1.0.0/README.md b/primerschemes/hbv/500/v1.0.0/README.md index ea430bf..72360b2 100644 --- a/primerschemes/hbv/500/v1.0.0/README.md +++ b/primerschemes/hbv/500/v1.0.0/README.md @@ -1,5 +1,9 @@ # hbv 500bp v1.0.0 +## Description + +Schemes generated for the Hepatitis B virus (hbv) + ## Overviews ![NC_003977.2.png](work/NC_003977.2.png) @@ -8,25 +12,25 @@ ```json { - "algorithmversion": "1.1.2", "ampliconsize": 500, + "schemeversion": "v1.0.0", + "schemename": "hbv", + "primer_bed_md5": "f1874f2b2332dff4b4cd6f0075f128dd", + "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", + "status": "draft", + "citations": [], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "f1874f2b2332dff4b4cd6f0075f128dd", - "reference.fasta.md5": "7612eab3e2389215206ae17187da1791", - "schemename": "hbv", - "schemeversion": "v1.0.0", - "status": "draft" + "algorithmversion": "primaldigest:1.1.2", + "species": [ + 10407 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the Hepatitis B virus (hbv)" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/hbv/500/v1.0.0/info.json b/primerschemes/hbv/500/v1.0.0/info.json index 2add84f..d959ec8 100644 --- a/primerschemes/hbv/500/v1.0.0/info.json +++ b/primerschemes/hbv/500/v1.0.0/info.json @@ -6,9 +6,15 @@ "artic network" ], "citations": [], - "primer.bed.md5": "f1874f2b2332dff4b4cd6f0075f128dd", - "reference.fasta.md5": "7612eab3e2389215206ae17187da1791", + "primer_bed_md5": "f1874f2b2332dff4b4cd6f0075f128dd", + "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", "schemename": "hbv", "schemeversion": "v1.0.0", - "status": "draft" + "status": "draft", + "species": [10407], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the Hepatitis B virus (hbv)" } + diff --git a/primerschemes/hbv/500/v1.0.0/work/config.json b/primerschemes/hbv/500/v1.0.0/work/config.json index 1dd5354..69045be 100644 --- a/primerschemes/hbv/500/v1.0.0/work/config.json +++ b/primerschemes/hbv/500/v1.0.0/work/config.json @@ -31,7 +31,7 @@ "npools": 2, "plot": true, "primaldigest_version": "1.1.2", - "primer.bed.md5": "f1874f2b2332dff4b4cd6f0075f128dd", + "primer_bed_md5": "f1874f2b2332dff4b4cd6f0075f128dd", "primer_gc_max": 55, "primer_gc_min": 30, "primer_hairpin_th_max": 47.0, diff --git a/primerschemes/hbv/500/v1.1.0/README.md b/primerschemes/hbv/500/v1.1.0/README.md index 87ca850..41616db 100644 --- a/primerschemes/hbv/500/v1.1.0/README.md +++ b/primerschemes/hbv/500/v1.1.0/README.md @@ -1,5 +1,9 @@ # hbv 500bp v1.1.0 +## Description + +Schemes generated for the Hepatitis B virus (hbv) + ## Overviews ![NC_003977.2.png](work/NC_003977.2.png) @@ -8,25 +12,25 @@ ```json { - "algorithmversion": "1.1.3", "ampliconsize": 500, + "schemeversion": "v1.1.0", + "schemename": "hbv", + "primer_bed_md5": "dd96ade2e5c59377808368cc116a8361", + "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", + "status": "draft", + "citations": [], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "dd96ade2e5c59377808368cc116a8361", - "reference.fasta.md5": "7612eab3e2389215206ae17187da1791", - "schemename": "hbv", - "schemeversion": "v1.1.0", - "status": "draft" + "algorithmversion": "primaldigest:1.1.3", + "species": [ + 10407 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the Hepatitis B virus (hbv)" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/hbv/500/v1.1.0/info.json b/primerschemes/hbv/500/v1.1.0/info.json index a60ea0a..ee12e58 100644 --- a/primerschemes/hbv/500/v1.1.0/info.json +++ b/primerschemes/hbv/500/v1.1.0/info.json @@ -1,14 +1,21 @@ { - "algorithmversion": "primaldigest:1.1.3", "ampliconsize": 500, + "schemeversion": "v1.1.0", + "schemename": "hbv", + "primer_bed_md5": "dd96ade2e5c59377808368cc116a8361", + "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", + "status": "draft", + "citations": [], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "dd96ade2e5c59377808368cc116a8361", - "reference.fasta.md5": "7612eab3e2389215206ae17187da1791", - "schemename": "hbv", - "schemeversion": "v1.1.0", - "status": "draft" -} + "algorithmversion": "primaldigest:1.1.3", + "species": [ + 10407 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the Hepatitis B virus (hbv)" +} \ No newline at end of file diff --git a/primerschemes/hbv/500/v1.1.0/work/config.json b/primerschemes/hbv/500/v1.1.0/work/config.json index 2c02bca..ab9079b 100644 --- a/primerschemes/hbv/500/v1.1.0/work/config.json +++ b/primerschemes/hbv/500/v1.1.0/work/config.json @@ -32,7 +32,7 @@ "npools": 2, "plot": true, "primaldigest_version": "1.1.3", - "primer.bed.md5": "dd96ade2e5c59377808368cc116a8361", + "primer_bed_md5": "dd96ade2e5c59377808368cc116a8361", "primer_gc_max": 55, "primer_gc_min": 30, "primer_hairpin_th_max": 47.0, @@ -42,5 +42,5 @@ "primer_tm_max": 62.5, "primer_tm_min": 59.5, "reducekmers": false, - "reference.fasta.md5": "7612eab3e2389215206ae17187da1791" + "reference_fasta_md5": "7612eab3e2389215206ae17187da1791" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v1.0.0/README.md b/primerschemes/sars-cov-2/400/v1.0.0/README.md index 61f52db..6602512 100644 --- a/primerschemes/sars-cov-2/400/v1.0.0/README.md +++ b/primerschemes/sars-cov-2/400/v1.0.0/README.md @@ -1,30 +1,36 @@ # sars-cov-2 400bp v1.0.0 +## Description + +Schemes generated for the SARs-CoV-2 Outbreak + ## Overviews ## Details ```json { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v1.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "907d8d0e3efecd82e07120eda2b70d89", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [ + "https://doi.org/10.1038/nprot.2017.066" + ], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "907d8d0e3efecd82e07120eda2b70d89", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v1.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v1.0.0/info.json b/primerschemes/sars-cov-2/400/v1.0.0/info.json index 2da5059..48d36a6 100644 --- a/primerschemes/sars-cov-2/400/v1.0.0/info.json +++ b/primerschemes/sars-cov-2/400/v1.0.0/info.json @@ -1,14 +1,23 @@ { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v1.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "907d8d0e3efecd82e07120eda2b70d89", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [ + "https://doi.org/10.1038/nprot.2017.066" + ], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "907d8d0e3efecd82e07120eda2b70d89", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v1.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v1.0.0/work/config.json b/primerschemes/sars-cov-2/400/v1.0.0/work/config.json index 1203522..64cadc2 100644 --- a/primerschemes/sars-cov-2/400/v1.0.0/work/config.json +++ b/primerschemes/sars-cov-2/400/v1.0.0/work/config.json @@ -6,8 +6,8 @@ "quick.lab" ], "citation": "na", - "primer.bed.md5": "907d8d0e3efecd82e07120eda2b70d89", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "primer_bed_md5": "907d8d0e3efecd82e07120eda2b70d89", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "schemename": "sars-cov-2", "schemeversion": "v1.0.0", "validated": true diff --git a/primerschemes/sars-cov-2/400/v2.0.0/README.md b/primerschemes/sars-cov-2/400/v2.0.0/README.md index 2716baa..3cefd14 100644 --- a/primerschemes/sars-cov-2/400/v2.0.0/README.md +++ b/primerschemes/sars-cov-2/400/v2.0.0/README.md @@ -1,30 +1,36 @@ # sars-cov-2 400bp v2.0.0 +## Description + +Schemes generated for the SARs-CoV-2 Outbreak + ## Overviews ## Details ```json { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v2.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "c9916963e43951541e8a11274e0ac0df", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [ + "https://doi.org/10.1038/nprot.2017.066" + ], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "c9916963e43951541e8a11274e0ac0df", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v2.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v2.0.0/info.json b/primerschemes/sars-cov-2/400/v2.0.0/info.json index 696634e..b7b2755 100644 --- a/primerschemes/sars-cov-2/400/v2.0.0/info.json +++ b/primerschemes/sars-cov-2/400/v2.0.0/info.json @@ -1,14 +1,23 @@ { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v2.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "c9916963e43951541e8a11274e0ac0df", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [ + "https://doi.org/10.1038/nprot.2017.066" + ], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "c9916963e43951541e8a11274e0ac0df", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v2.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v2.0.0/work/config.json b/primerschemes/sars-cov-2/400/v2.0.0/work/config.json index efeaf77..7dddbc4 100644 --- a/primerschemes/sars-cov-2/400/v2.0.0/work/config.json +++ b/primerschemes/sars-cov-2/400/v2.0.0/work/config.json @@ -6,8 +6,8 @@ "quick.lab" ], "citation": "na", - "primer.bed.md5": "c9916963e43951541e8a11274e0ac0df", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "primer_bed_md5": "c9916963e43951541e8a11274e0ac0df", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "schemename": "sars-cov-2", "schemeversion": "v2.0.0", "validated": true diff --git a/primerschemes/sars-cov-2/400/v3.0.0/README.md b/primerschemes/sars-cov-2/400/v3.0.0/README.md index 4e497ce..aefbfa8 100644 --- a/primerschemes/sars-cov-2/400/v3.0.0/README.md +++ b/primerschemes/sars-cov-2/400/v3.0.0/README.md @@ -1,30 +1,36 @@ # sars-cov-2 400bp v3.0.0 +## Description + +Schemes generated for the SARs-CoV-2 Outbreak + ## Overviews ## Details ```json { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v3.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "03e1c3eecc21bdb66a4bec990e0225cc", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [ + "https://doi.org/10.1038/nprot.2017.066" + ], "authors": [ - "quick lab", - "artic network" + "artic network", + "quick lab" ], - "citations": [], - "primer.bed.md5": "03e1c3eecc21bdb66a4bec990e0225cc", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v3.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v3.0.0/info.json b/primerschemes/sars-cov-2/400/v3.0.0/info.json index 24d9d91..1bd2fdf 100644 --- a/primerschemes/sars-cov-2/400/v3.0.0/info.json +++ b/primerschemes/sars-cov-2/400/v3.0.0/info.json @@ -1,14 +1,23 @@ { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v3.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "03e1c3eecc21bdb66a4bec990e0225cc", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [ + "https://doi.org/10.1038/nprot.2017.066" + ], "authors": [ - "quick lab", - "artic network" + "artic network", + "quick lab" ], - "citations": [], - "primer.bed.md5": "03e1c3eecc21bdb66a4bec990e0225cc", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v3.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v3.0.0/work/config.json b/primerschemes/sars-cov-2/400/v3.0.0/work/config.json index db38066..e0e989a 100644 --- a/primerschemes/sars-cov-2/400/v3.0.0/work/config.json +++ b/primerschemes/sars-cov-2/400/v3.0.0/work/config.json @@ -6,8 +6,8 @@ "quick.lab" ], "citation": "na", - "primer.bed.md5": "03e1c3eecc21bdb66a4bec990e0225cc", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "primer_bed_md5": "03e1c3eecc21bdb66a4bec990e0225cc", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "schemename": "sars-cov-2", "schemeversion": "v3.0.0", "validated": true diff --git a/primerschemes/sars-cov-2/400/v4.0.0/README.md b/primerschemes/sars-cov-2/400/v4.0.0/README.md index d815049..b3c1fdb 100644 --- a/primerschemes/sars-cov-2/400/v4.0.0/README.md +++ b/primerschemes/sars-cov-2/400/v4.0.0/README.md @@ -1,30 +1,34 @@ # sars-cov-2 400bp v4.0.0 +## Description + +Schemes generated for the SARs-CoV-2 Outbreak + ## Overviews ## Details ```json { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v4.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "6c42c61f304702adc6c550ad0941ed6f", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "6c42c61f304702adc6c550ad0941ed6f", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v4.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v4.0.0/info.json b/primerschemes/sars-cov-2/400/v4.0.0/info.json index f39d057..110584f 100644 --- a/primerschemes/sars-cov-2/400/v4.0.0/info.json +++ b/primerschemes/sars-cov-2/400/v4.0.0/info.json @@ -1,14 +1,21 @@ { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v4.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "6c42c61f304702adc6c550ad0941ed6f", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "6c42c61f304702adc6c550ad0941ed6f", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v4.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v4.0.0/work/config.json b/primerschemes/sars-cov-2/400/v4.0.0/work/config.json index ac11559..8e80ad1 100644 --- a/primerschemes/sars-cov-2/400/v4.0.0/work/config.json +++ b/primerschemes/sars-cov-2/400/v4.0.0/work/config.json @@ -6,8 +6,8 @@ "quick.lab" ], "citation": "na", - "primer.bed.md5": "6c42c61f304702adc6c550ad0941ed6f", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "primer_bed_md5": "6c42c61f304702adc6c550ad0941ed6f", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "schemename": "sars-cov-2", "schemeversion": "v4.0.0", "validated": true diff --git a/primerschemes/sars-cov-2/400/v4.1.0/README.md b/primerschemes/sars-cov-2/400/v4.1.0/README.md index c3602d9..3231fcf 100644 --- a/primerschemes/sars-cov-2/400/v4.1.0/README.md +++ b/primerschemes/sars-cov-2/400/v4.1.0/README.md @@ -1,30 +1,36 @@ # sars-cov-2 400bp v4.1.0 +## Description + +Schemes generated for the SARs-CoV-2 Outbreak + ## Overviews ## Details ```json { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v4.1.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [ + "https://doi.org/10.1038/nprot.2017.066" + ], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v4.1.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v4.1.0/info.json b/primerschemes/sars-cov-2/400/v4.1.0/info.json index 23e905b..36dbbe9 100644 --- a/primerschemes/sars-cov-2/400/v4.1.0/info.json +++ b/primerschemes/sars-cov-2/400/v4.1.0/info.json @@ -1,14 +1,23 @@ { - "algorithmversion": "primalscheme1:1.0.0", "ampliconsize": 400, + "schemeversion": "v4.1.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [ + "https://doi.org/10.1038/nprot.2017.066" + ], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v4.1.0", - "status": "deprecated" + "algorithmversion": "primalscheme1:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v4.1.0/work/config.json b/primerschemes/sars-cov-2/400/v4.1.0/work/config.json index a53b8a3..0d12f7f 100644 --- a/primerschemes/sars-cov-2/400/v4.1.0/work/config.json +++ b/primerschemes/sars-cov-2/400/v4.1.0/work/config.json @@ -6,8 +6,8 @@ "quick.lab" ], "citation": "na", - "primer.bed.md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "primer_bed_md5": "98ffdb9c0e31f2c1c819c7a4d2c8a048", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "schemename": "sars-cov-2", "schemeversion": "v4.1.0", "validated": true diff --git a/primerschemes/sars-cov-2/400/v5.0.0/README.md b/primerschemes/sars-cov-2/400/v5.0.0/README.md index 3fcd9ca..03b8ee6 100644 --- a/primerschemes/sars-cov-2/400/v5.0.0/README.md +++ b/primerschemes/sars-cov-2/400/v5.0.0/README.md @@ -1,30 +1,34 @@ # sars-cov-2 400bp v5.0.0 +## Description + +Schemes generated for the SARs-CoV-2 Outbreak + ## Overviews ## Details ```json { - "algorithmversion": "primalscheme2:1.0.0", "ampliconsize": 400, + "schemeversion": "v5.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "6292814b0ec248605c72707d34dda1eb", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "6292814b0ec248605c72707d34dda1eb", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v5.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme2:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v5.0.0/info.json b/primerschemes/sars-cov-2/400/v5.0.0/info.json index 57644ca..1ba35b1 100644 --- a/primerschemes/sars-cov-2/400/v5.0.0/info.json +++ b/primerschemes/sars-cov-2/400/v5.0.0/info.json @@ -1,14 +1,21 @@ { - "algorithmversion": "primalscheme2:1.0.0", "ampliconsize": 400, + "schemeversion": "v5.0.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "6292814b0ec248605c72707d34dda1eb", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [], "authors": [ "quick lab", "artic network" ], - "citations": [], - "primer.bed.md5": "6292814b0ec248605c72707d34dda1eb", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v5.0.0", - "status": "deprecated" + "algorithmversion": "primalscheme2:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v5.0.0/work/config.json b/primerschemes/sars-cov-2/400/v5.0.0/work/config.json index bd2bbd0..74ec240 100644 --- a/primerschemes/sars-cov-2/400/v5.0.0/work/config.json +++ b/primerschemes/sars-cov-2/400/v5.0.0/work/config.json @@ -6,8 +6,8 @@ "quick.lab" ], "citation": "na", - "primer.bed.md5": "6292814b0ec248605c72707d34dda1eb", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "primer_bed_md5": "6292814b0ec248605c72707d34dda1eb", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "schemename": "sars-cov-2", "schemeversion": "v5.0.0", "validated": true diff --git a/primerschemes/sars-cov-2/400/v5.2.0/README.md b/primerschemes/sars-cov-2/400/v5.2.0/README.md index 4ff1ff2..24f81e1 100644 --- a/primerschemes/sars-cov-2/400/v5.2.0/README.md +++ b/primerschemes/sars-cov-2/400/v5.2.0/README.md @@ -1,30 +1,34 @@ # sars-cov-2 400bp v5.2.0 +## Description + +Schemes generated for the SARs-CoV-2 Outbreak + ## Overviews ## Details ```json { - "algorithmversion": "primalscheme2:1.0.0", "ampliconsize": 400, + "schemeversion": "v5.2.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "6de462d8ffffcfb2aa37f7eeb205d94b", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [], "authors": [ - "quick lab", - "artic network" + "artic network", + "quick lab" ], - "citations": [], - "primer.bed.md5": "6de462d8ffffcfb2aa37f7eeb205d94b", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v5.2.0", - "status": "deprecated" + "algorithmversion": "primalscheme2:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v5.2.0/info.json b/primerschemes/sars-cov-2/400/v5.2.0/info.json index 7b0f279..a465c58 100644 --- a/primerschemes/sars-cov-2/400/v5.2.0/info.json +++ b/primerschemes/sars-cov-2/400/v5.2.0/info.json @@ -1,14 +1,21 @@ { - "algorithmversion": "primalscheme2:1.0.0", "ampliconsize": 400, + "schemeversion": "v5.2.0", + "schemename": "sars-cov-2", + "primer_bed_md5": "6de462d8ffffcfb2aa37f7eeb205d94b", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "deprecated", + "citations": [], "authors": [ - "quick lab", - "artic network" + "artic network", + "quick lab" ], - "citations": [], - "primer.bed.md5": "6de462d8ffffcfb2aa37f7eeb205d94b", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v5.2.0", - "status": "deprecated" + "algorithmversion": "primalscheme2:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v5.2.0/work/config.json b/primerschemes/sars-cov-2/400/v5.2.0/work/config.json index cc78be4..04d792c 100644 --- a/primerschemes/sars-cov-2/400/v5.2.0/work/config.json +++ b/primerschemes/sars-cov-2/400/v5.2.0/work/config.json @@ -6,8 +6,8 @@ "quick.lab" ], "citation": "na", - "primer.bed.md5": "6de462d8ffffcfb2aa37f7eeb205d94b", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "primer_bed_md5": "6de462d8ffffcfb2aa37f7eeb205d94b", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "schemename": "sars-cov-2", "schemeversion": "v5.2.0", "validated": true diff --git a/primerschemes/sars-cov-2/400/v5.3.2/README.md b/primerschemes/sars-cov-2/400/v5.3.2/README.md index 72c0f04..9711c21 100644 --- a/primerschemes/sars-cov-2/400/v5.3.2/README.md +++ b/primerschemes/sars-cov-2/400/v5.3.2/README.md @@ -1,31 +1,35 @@ # sars-cov-2 400bp v5.3.2 +## Description + +Schemes generated for the SARs-CoV-2 Outbreak + ## Overviews ## Details ```json { - "algorithmversion": "primalscheme2:1.0.0", "ampliconsize": 400, + "schemeversion": "v5.3.2", + "schemename": "sars-cov-2", + "primer_bed_md5": "722d56c381bf301aa9c5ae8721c78063", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "validated", + "citations": [], "authors": [ - "quick lab", "artic network", + "quick lab", "bccdc" ], - "citations": [], - "primer.bed.md5": "722d56c381bf301aa9c5ae8721c78063", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v5.3.2", - "status": "validated" + "algorithmversion": "primalscheme2:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } ``` - - ------------------------------------------------------------------------- - -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) \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v5.3.2/info.json b/primerschemes/sars-cov-2/400/v5.3.2/info.json index 80a20b3..8e52d58 100644 --- a/primerschemes/sars-cov-2/400/v5.3.2/info.json +++ b/primerschemes/sars-cov-2/400/v5.3.2/info.json @@ -1,15 +1,22 @@ { - "algorithmversion": "primalscheme2:1.0.0", "ampliconsize": 400, + "schemeversion": "v5.3.2", + "schemename": "sars-cov-2", + "primer_bed_md5": "722d56c381bf301aa9c5ae8721c78063", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "status": "validated", + "citations": [], "authors": [ - "quick lab", "artic network", + "quick lab", "bccdc" ], - "citations": [], - "primer.bed.md5": "722d56c381bf301aa9c5ae8721c78063", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", - "schemename": "sars-cov-2", - "schemeversion": "v5.3.2", - "status": "validated" + "algorithmversion": "primalscheme2:1.0.0", + "species": [ + 2697049 + ], + "license": "CC-BY-4.0", + "primerclass": "primerschemes", + "infoschema": "v1.0.0", + "description": "Schemes generated for the SARs-CoV-2 Outbreak" } \ No newline at end of file diff --git a/primerschemes/sars-cov-2/400/v5.3.2/work/config.json b/primerschemes/sars-cov-2/400/v5.3.2/work/config.json index 97de6df..2dc7abd 100644 --- a/primerschemes/sars-cov-2/400/v5.3.2/work/config.json +++ b/primerschemes/sars-cov-2/400/v5.3.2/work/config.json @@ -7,8 +7,8 @@ "bccdc" ], "citation": "na", - "primer.bed.md5": "722d56c381bf301aa9c5ae8721c78063", - "reference.fasta.md5": "7f8995394dfc7d5ffeb9fe8322ade58c", + "primer_bed_md5": "722d56c381bf301aa9c5ae8721c78063", + "reference_fasta_md5": "7f8995394dfc7d5ffeb9fe8322ade58c", "schemename": "sars-cov-2", "schemeversion": "v5.3.2", "validated": true From 886d59205753ffdccefbf408e3a2535873139924 Mon Sep 17 00:00:00 2001 From: ChrisgKent Date: Fri, 27 Oct 2023 15:57:38 +0000 Subject: [PATCH 2/2] Auto updating index --- index.json | 106 ++++++++++++++++++++++++++++++++++++++--------------- 1 file changed, 77 insertions(+), 29 deletions(-) diff --git a/index.json b/index.json index 678a3c0..eaf1422 100644 --- a/index.json +++ b/index.json @@ -10,12 +10,16 @@ "artic network" ], "citations": [], - "config.json.md5": "4137d7ad6f0cc949be434fdb3480eef9", - "config.json.url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/work/config.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/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/primer.bed", + "primerclass": "primerschemes", "reference_fasta_md5": "7612eab3e2389215206ae17187da1791", "reference_fasta_url": "https://raw.githubusercontent.com/ChrisgKent/primerschemes/main/primerschemes/hbv/500/v1.0.0/reference.fasta", + "species": [ + 10407 + ], "status": "draft" }, "v1.1.0": { @@ -25,12 +29,16 @@ "artic network" ], "citations": [], - 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