From 785a6c4f5ed0d368b2f8879c0bd5ad66040eda39 Mon Sep 17 00:00:00 2001 From: ChrisKent Date: Thu, 14 Dec 2023 15:13:47 +0000 Subject: [PATCH] Version v1.0.0 --- README.md | 9 + dist/primal_page-1.0.0-py3-none-any.whl | Bin 13436 -> 13668 bytes dist/primal_page-1.0.0.tar.gz | Bin 10670 -> 11331 bytes index.json | 333 ++++++++- poetry.lock | 657 +++++++++--------- .../__pycache__/build_index.cpython-311.pyc | Bin 9287 -> 9954 bytes primal_page/__pycache__/main.cpython-311.pyc | Bin 28883 -> 29266 bytes .../__pycache__/schemas.cpython-311.pyc | Bin 4262 -> 6173 bytes primal_page/build_index.py | 26 +- primal_page/main.py | 61 +- primal_page/schemas.py | 45 ++ primal_page/search.py | 40 -- pyproject.toml | 1 + 13 files changed, 773 insertions(+), 399 deletions(-) delete mode 100644 primal_page/search.py diff --git a/README.md b/README.md index 9e065a7..e412dc5 100644 --- a/README.md +++ b/README.md @@ -27,3 +27,12 @@ This is the tooling for working with the primerschemes index The main purpose of info.json is to store vital metadata, which is parsed into the repo-manifest. +### Create + +The create command has two main modes of use. +- Where the scheme directory is provided, and used to parse; --primerbed, --reference, --configpath, --algorithmversion. +- The options are provided via the CLI + +If a field cannot be parsed via the scheme directory, it will require it to be spesified via the CLI. +- CLI args always override the parsed args. + diff --git a/dist/primal_page-1.0.0-py3-none-any.whl b/dist/primal_page-1.0.0-py3-none-any.whl index e06c843dac19ee9c013568f745d8eaf6d8dcf615..8e00ff365529fa247a3ff9447859e1fbd9e94a3e 100644 GIT binary patch delta 9456 zcmY+Kbxhttv$h|!xV!5E6nA&G;_gt~p}72@I24!S?(XjH?(XgsX@T_lk|kxNgQuZ0occGw4(pLHtM4lp@b^W1X~9(?Lvkb zG7as`@>8w&vmyni(CS4qz*Aw@bgX{(vr`S>M!e3GeflO`N$tFSvgagaGc7(tjbAFz zG-a}My73X-ol!lcq41ODGuD!gMxE}~lH$aCdx2$hw+{NtK-f^*ANI8`i@cjfwoRVa zhd{(Hs0$8xDGYy^8nXC3oL}_uxX-~z_YYEtyhU>+znJ!$v@X?PVvUKvI 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zSh8x@HbEvQSY}asksk+EOn=L@U+~@d%=M)pjOnY*pVY-{+#QUg$)Te?$$r>Occxm6PbEG!?8&6Fv2JT{w?AG1pM;yGYDAS z&D&wQVdg~DXG2VT)!*98%;z(4m&pkM$1 delta 1039 zcmZXT&rcIU6vt<_rOEOZq0NHk%Js0 zUQA4I4xUWlU`>SRfq2(Mj~>13A7J9YpcmiU781%N`{{e{``(+`H`{lYYrXmhP4f|0 zKPNZ&ci*laqsne-Zd)OMN%@nh!Mp8BJp<*O|ukH8<0D+_?Y? zocQhFx3eG*a$~EN5Xfp+kZXVza{7j#ZrcJ{lYUo)w}j(p2<8RRw3(BSO+vlPzhm zHdK8s01irDjg1Cyf zhPaNnfw+kn2mEmZ($w}8OvX(sos=)bvkN#t+s(~tNx&b1h>M66!a1jNl^JwT-pqCv z3l&SuU=XL`98Wl(M7JD`^bO*+wkywA)64vA8!wevwa6#L3Z&q*R-*Dnq str: return hash_md5.hexdigest() -def validate_primer_bed(primer_bed: pathlib.Path, fix: bool = False): +def validate_primer_bed(primer_bed: pathlib.Path, fix: bool = False) -> bool: """Validate a primer bed file""" with open(primer_bed, "r") as f: for lineindex, line in enumerate(f.readlines()): @@ -73,14 +78,20 @@ def validate_primer_bed(primer_bed: pathlib.Path, fix: bool = False): ) # Check for valid primername - primername = data[3].split("_") - if len(primername) == 4 and primername[-1].isdigit(): - # Valid name - pass - else: - raise ValueError( - f"Line {lineindex} in {primer_bed} does not have a valid primername '{data[3]}'" - ) + raw_primername = data[3].strip() + + match determine_primername_version(raw_primername): + case PrimerNameVersion.V1: + # Valid name + pass + case PrimerNameVersion.V2: + # Valid version 2 name + pass + case PrimerNameVersion.INVALID: + raise ValueError( + f"Line {lineindex} in {primer_bed} does not have a valid primername '{raw_primername}'" + ) + return True @@ -219,14 +230,14 @@ def create( "artic network", ], primerbed: Annotated[ - pathlib.Path, + Optional[pathlib.Path], typer.Option( help="Manually specify the primer bed file, default is *primer.bed", readable=True, ), ] = None, reference: Annotated[ - pathlib.Path, + Optional[pathlib.Path], typer.Option( help="Manually specify the referance.fasta file, default is *.fasta", readable=True, @@ -237,19 +248,20 @@ def create( typer.Option(help="Where to output the scheme", writable=True), ] = pathlib.Path("primerschemes"), configpath: Annotated[ - pathlib.Path, + Optional[pathlib.Path], typer.Option( help="Where the config.json file is located", readable=True, exists=True ), ] = None, algorithmversion: Annotated[ - str, typer.Option(help="The version of primalscheme or other") + Optional[str], typer.Option(help="The version of primalscheme or other") ] = None, description: Annotated[ - str, typer.Option(help="A description of the scheme") + Optional[str], typer.Option(help="A description of the scheme") ] = None, derivedfrom: Annotated[ - str, typer.Option(help="Which scheme has this scheme been derived from") + Optional[str], + typer.Option(help="Which scheme has this scheme been derived from"), ] = None, primerclass: Annotated[ PrimerClass, typer.Option(help="The primer class") @@ -555,16 +567,19 @@ def remove_citation( def build_index( gitaccount: Annotated[ str, - typer.Argument(help="The name of the github account"), + typer.Option(help="The name of the github account"), ] = "quick-lab", gitserver: Annotated[ str, - typer.Argument(help="The name of the github server"), + typer.Option(help="The name of the github server"), ] = "https://github.com/", + parentdir: Annotated[ + pathlib.Path, typer.Option(help="The parent directory") + ] = pathlib.Path("."), ): """Build an index.json file from all schemes in the directory""" - create_index(gitserver, gitaccount) + create_index(gitserver, gitaccount, parentdir) @app.command() diff --git a/primal_page/schemas.py b/primal_page/schemas.py index 49afef8..68b319c 100644 --- a/primal_page/schemas.py +++ b/primal_page/schemas.py @@ -7,6 +7,51 @@ SCHEMENAME_PATTERN = r"^[a-z0-9][a-z0-9-]*[a-z0-9]$" VERSION_PATTERN = r"^v\d+\.\d+\.\d+$" +# Primername versions +V2_PRIMERNAME = r"^[a-zA-Z0-9\-]+_[0-9]+_(LEFT|RIGHT)_[0-9]+$" +V1_PRIMERNAME = r"^[a-zA-Z0-9\-]+_[0-9]+_(LEFT|RIGHT)(_ALT|_alt)*$" + + +class PrimerNameVersion(Enum): + V1 = "v1" + V2 = "v2" + INVALID = "invalid" # Not applicable + + +def determine_primername_version(primername: str) -> PrimerNameVersion: + """ + Determine the primername version + :param primername: The primername to check + :return: The primername version + """ + if re.search(V2_PRIMERNAME, primername): + return PrimerNameVersion.V2 + elif re.search(V1_PRIMERNAME, primername): + return PrimerNameVersion.V1 + else: + return PrimerNameVersion.INVALID + + +def convert_v1_primernames_to_v2(primername: str) -> str: + """ + Convert a v1 primername to a v2 primername. Cannot handle alt primers + :param primername: The v1 primername + :return: The v2 primername + """ + # Check if this is a v1 primername + if determine_primername_version(primername) != PrimerNameVersion.V1: + raise ValueError(f"{primername} is not a valid v1 primername") + + # Split the primername + data = primername.split("_") + # Remove the alt + if data[-1] == "alt" or data[-1] == "ALT": + raise ValueError(f"{primername} is a v1 alt primername, cannot convert") + + data.append("0") + # Join back together + return "_".join(data) + class PrimerClass(Enum): PRIMERSCHEMES = "primerschemes" diff --git a/primal_page/search.py b/primal_page/search.py deleted file mode 100644 index 58fa13d..0000000 --- a/primal_page/search.py +++ /dev/null @@ -1,40 +0,0 @@ -import json - -from primal_page.schemas import SchemeStatus - - -def depth_first_search(indexjson) -> tuple[str, str, int, str, dict]: - for pclass in indexjson: - for schemename in indexjson[pclass]: - for ampliconsize in indexjson[pclass][schemename]: - for version in indexjson[pclass][schemename][ampliconsize]: - yield pclass, schemename, ampliconsize, version, indexjson[pclass][ - schemename - ][ampliconsize][version] - - -def main(): - # Read in the index - # Will be a request to github - path_to_index = "/Users/kentcg/primerschemes-fork/index.json" - - index = json.load(open(path_to_index)) - - q_status = "deprecated" - - # Search parameters - # Search by status - - if q_status not in set(item.value for item in SchemeStatus): - print(f"Invalid status: {q_status}") - exit(1) - - for pclass, schemename, ampliconsize, scheme_version, info in depth_first_search( - index - ): - if info["status"] == q_status: - print(schemename, ampliconsize, scheme_version, pclass) - - -if __name__ == "__main__": - main() diff --git a/pyproject.toml b/pyproject.toml index 368dd7c..5356beb 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -15,6 +15,7 @@ typer = {extras = ["all"], version = "^0.9.0"} [tool.poetry.group.dev.dependencies] pytest = "^7.4.3" +typer-cli = {path = "../typer-cli"} # https://github.com/Patarimi/typer-cli/commit/f44b547a0b9ea71e5c7b2dc7d4c1ab1212394e5e [build-system] requires = ["poetry-core"]