Tooling and schemas for the primerschemes index

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Project links

Project description

Primal-Page

Tooling and schemas for the primerschemes index

Installation

pip install primal-page

Quick Start

Each version of a primerscheme has three parts; {schemename}/{ampliconsize}/{version}, which when combined these form the schemes unique identifier.

For a scheme to be added to the repo it requires three essential files.

primer.bed: Contains the primer information.
reference.fasta: Contains the reference genomes.
info.json: Contains key metadata for the scheme.

The primal-page create command will generates the info.json and parses a bed file and a fasta file into primer.bed and reference.fasta

Additional files are copied into the schemes work directory.

Example

Adding a minimal scheme

For a simple scheme, only fasta file (--reference) and a bed file (--primerbed) are required. Alongside metadata of --schemename, --algorithmversion, --species, --authors.

primal-page create \
    --schemename example-scheme \
    --algorithmversion ps:100 \
    --ampliconsize 500 \
    --species 123  \
    --schemeversion v1.0.0 \
    --primerbed ~/'minimal-scheme/minimal.bed' \
    --reference '~/minimal-scheme/ref.fasta' \
    --authors "me" \
    --authors "you" /
    '~/minimal-scheme'

Adding a custom scheme to quick-lab/primerschemes

create a local fork of https://github.com/quick-lab/primerschemes

Add the files to the forks primerschemes folder

primal-page create primal-page create ... --output ~/primerschemes/primerschemes

Create a pull request

New Schemas

info.json

This is the main metadata file for each primerscheme.

ampliconsize: PositiveInt
schemeversion: Following format listed below
schemename: Following format listed below
primer_bed_md5: MD5 hash of the schemes primer.bed file
reference_fasta_md5: MD5 hash of the schemes reference.fasta file
status:
- withdrawn: Removed due to major issue
- deprecated: Newer scheme is recommended
- autogenerated: Scheme has been autogenerated using species-agnostic pipelines
- draft: Scheme has been inspected in silico
- tested: Scheme has been tested in the laboratory
- validated: Scheme has been validated and/or published
citations: How the scheme should be cited if used. DOI links are recommended, however, tweets/blogs are all allowed
authors: The person or organization who generated the scheme. It is recommended that only corresponding/primary authors are included, with all other contributors recognized in the citations field
algorithmversion: The algorithm and the version used to generate the scheme
species: A list of organisms targeted by this scheme. NCBI TaxIds are recommend
license: The name of the license the primerscheme is offered under
primerclass: The class of scheme. Only primerscheme at the moment
infoschema: The version of the info.json
articbedversion: The version of the primer.bed (See below)
description: A free text description to describe the primerscheme
derivedfrom: To show if this scheme has been based on another primerscheme.
collections: A collection of vocabulary to provide filtering/grouping of schemes.
- ARTIC: Developed with the ARTIC network
- MODJADJI: Developed with MODJADJI
- QUICK-LAB: Developed with QUICK-LAB
- COMMUNITY: Developed by the COMMUNITY
- WASTE-WATER: Scheme capable of recovering genomes from high Ct samples (~30) samples, like wastewater. Typically 400bp schemes
- CLINICAL-ISOLATES: Scheme capable of recovering genomes from medium Ct samples (~25) samples. Typically ~1000bp schemes
- WHOLE-GENOME: Scheme that can theoretically recover a full genome
- PANEL: Scheme that can recover sections of a target genome
- MULTI-TARGET: Scheme that contains more than one target

PrimerNames Versions

Expected primernames (col3) in the primer.bed file

`V1`

This is the first standard for primernames. It follows the general pattern of {scheme-name|uuid}_{amplicon-number}_{LEFT|RIGHT} and an optional {_alt} to denote spike in primers.

Regex:

V1_PRIMERNAME = r"^[a-zA-Z0-9\-]+_[0-9]+_(LEFT|RIGHT)(_ALT[0-9]*|_alt[0-9]*)*$"

Example:

SARS-CoV-2_10_LEFT
SARS-CoV-2_10_LEFT_alt1

`V2`

This follows the pattern of {scheme-name|uuid}_{amplicon-number}_{LEFT|RIGHT}_{primer-number}.

This now enforces that splitting on _ will produce a consistent length, allowing the safe indexing of attributes.
primer-number is not enforced to be continuous. Therefore, the _0 numbered primer should not be thought of as the original and all other numbers as alts.

Example:

SARS-CoV-2_10_LEFT_0
SARS-CoV-2_10_LEFT_1

Regex:

V2_PRIMERNAME = r"^[a-zA-Z0-9\-]+_[0-9]+_(LEFT|RIGHT)_[0-9]+$"

ARTIC-primer.bed Versions

These are rough guidelines for the format of the primer.bed file. The general format is based on the .bed file and maintains compatibility with other tools.

colnames and indexes:

0 - chrom: The name of the reference genome the primers are indexed to
1 - chromStart: 0-based inclusive start coordinate
2 - chromEnd: 0-based non-inclusive end coordinate
3 - primer-name: Name of each primer
4 - pool: The pool each primer should be added into. 1 based.
5 - strand: Either + (forward) or - (reverse) primer
6 - primer-sequence: The 5'-3' sequence of the primer

V1

Depreciated

This was the original 6-col bedfile used very early in PrimalSchemes development, which excluded primer-sequence.

V2

Legacy

This uses the 7 columns described above, alongside V1:primernames.

Single chrom (reference) is expected
No header lines

V3

Current

This uses the 7 columns described above, alongside V2:primernames.

Multiple chrom (references)
Circular primers are allowed. The start of x_LEFT can be greater than the end of x_RIGHT
Header lines are used. Denoted with the # character

Scheme Version

In the form of v{Major}.{Minor}.{Patch}

Major: New scheme being generated with differant input params
Minor: Change to primers. Either additional / removal of primers
Patch: No change to primers. Often used for rebalancing or change in formatting

Regex:

VERSION_PATTERN = r"^v\d+\.\d+\.\d+$"

Scheme Name

Must only contain a-z, 0-9, and -. Cannot start or end with -

Regex:

SCHEMENAME_PATTERN = r"^[a-z0-9][a-z0-9-]*[a-z0-9]$"

CLI

`primal-page`

Usage:

$ primal-page [OPTIONS] COMMAND [ARGS]...

Options:

--version
--install-completion: Install completion for the current shell.
--show-completion: Show completion for the current shell, to copy it or customize the installation.
--help: Show this message and exit.

Commands:

aliases: Manage aliases
build-index: Build an index.json file from all schemes...
create: Create a new scheme in the required format
dev: Development commands
download: Download schemes from the index.json
modify: Modify an existing scheme's metadata...
remove: Remove a scheme's version from the repo,...

`primal-page aliases`

Manage aliases

Usage:

$ primal-page aliases [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

add: Add an alias:schemename to the alias file
remove: Remove an alias from the alias file.

`primal-page aliases add`

Add an alias:schemename to the alias file

Usage:

$ primal-page aliases add [OPTIONS] ALIASES_FILE ALIAS SCHEMENAME

Arguments:

ALIASES_FILE: The path to the alias file to write to [required]
ALIAS: The alias to add [required]
SCHEMENAME: The schemename the alias refers to [required]

Options:

--help: Show this message and exit.

`primal-page aliases remove`

Remove an alias from the alias file. Does nothing if the alias does not exist

Usage:

$ primal-page aliases remove [OPTIONS] ALIASES_FILE ALIAS

Arguments:

ALIASES_FILE: The path to the alias file to write to [required]
ALIAS: The alias to add [required]

Options:

--help: Show this message and exit.

`primal-page build-index`

Build an index.json file from all schemes in the directory

Usage:

$ primal-page build-index [OPTIONS]

Options:

--gitaccount TEXT: The name of the github account [default: quick-lab]
--gitserver TEXT: The name of the github server [default: https://github.com/]
--parentdir PATH: The parent directory [default: .]
--git-commit-sha TEXT: The git commit
--force / --no-force: Force the creation of the index.json [default: no-force]
--help: Show this message and exit.

`primal-page create`

Create a new scheme in the required format

Usage:

$ primal-page create [OPTIONS] SCHEMEPATH

Arguments:

SCHEMEPATH: The path to the primerscheme directory [required]

Options:

--schemename TEXT: The name of the scheme [required]
--ampliconsize INTEGER RANGE: Amplicon size [x>=100; required]
--schemeversion TEXT: Scheme version, default is parsed from config.json [required]
--species INTEGER: The species this scheme targets. Please use NCBI taxonomy ids [required]
--authors TEXT: Any authors [required]
--schemestatus [withdrawn|deprecated|autogenerated|draft|tested|validated]: Scheme status [default: draft]
--citations TEXT: Any associated citations. Please use DOI
--primerbed PATH: Manually specify the primer bed file, default is *primer.bed
--reference PATH: Manually specify the reference.fasta file, default is *.fasta
--output PATH: Where to output the scheme [default: primerschemes]
--configpath PATH: Where the config.json file is located
--algorithmversion TEXT: The version of primalscheme or other
--description TEXT: A description of the scheme
--derivedfrom TEXT: Which scheme has this scheme been derived from
--primerclass [primerschemes]: The primer class [default: primerschemes]
--collection [ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET]: The collection
--link-protocol TEXT: Optional link to protocol
--link-validation TEXT: Optional link to validation data
--links-homepage TEXT: Optional link to homepage
--link-vendor TEXT: Optional link to vendors
--link-misc TEXT: Optional miscellaneous link
--fix / --no-fix: Attempt to fix the scheme [default: no-fix]
--help: Show this message and exit.

`primal-page download`

Download schemes from the index.json

Usage:

$ primal-page download [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

all: Download all schemes from the index.json
scheme: Download a scheme from the index.json

`primal-page download all`

Download all schemes from the index.json

Usage:

$ primal-page download all [OPTIONS]

Options:

--output PATH: The directory the primerschemes dir will be created in [required]
--index-url TEXT: The URL to the index.json [default: https://raw.githubusercontent.com/quick-lab/primerschemes/main/index.json]
--help: Show this message and exit.

`primal-page download scheme`

Download a scheme from the index.json

Usage:

$ primal-page download scheme [OPTIONS] SCHEMENAME AMPLICONSIZE SCHEMEVERSION

Arguments:

SCHEMENAME: The name of the scheme [required]
AMPLICONSIZE: Amplicon size [required]
SCHEMEVERSION: Scheme version [required]

Options:

--output PATH: The directory the primerschemes dir will be created in [required]
--index-url TEXT: The URL to the index.json [default: https://raw.githubusercontent.com/quick-lab/primerschemes/main/index.json]
--help: Show this message and exit.

`primal-page modify`

Modify an existing scheme's metadata (info.json)

Usage:

$ primal-page modify [OPTIONS] COMMAND [ARGS]...

Options:

--help: Show this message and exit.

Commands:

add-author: Append an author to the authors list in...
add-citation: Append an citation to the authors list in...
add-collection: Add a Collection to the Collection list in...
add-link: Add a link to the selected link field to...
change-contactinfo: Change the contactinfo field in the info.json
change-derivedfrom: Replaces the derivedfrom in the info.json...
change-description: Replaces the description in the info.json...
change-license: Replaces the license in the info.json file
change-primerclass: Change the primerclass field in the info.json
change-status: Change the status field in the info.json
regenerate: Validates the info.json and regenerate the...
remove-author: Remove an author from the authors list in...
remove-citation: Remove an citation form the authors list...
remove-collection: Remove an Collection from the Collection...
remove-link: Add a link to the selected link field to...
reorder-authors: Reorder the authors in the info.json file

`primal-page modify add-author`

Append an author to the authors list in the info.json file

Usage:

$ primal-page modify add-author [OPTIONS] SCHEMEINFO AUTHOR

Arguments:

SCHEMEINFO: The path to info.json [required]
AUTHOR: The author to add [required]

Options:

--author-index INTEGER: The 0-based index to insert the author at. Default is the end [required]
--help: Show this message and exit.

`primal-page modify add-citation`

Append an citation to the authors list in the info.json file

Usage:

$ primal-page modify add-citation [OPTIONS] SCHEMEINFO CITATION

Arguments:

SCHEMEINFO: The path to info.json [required]
CITATION: The citation to add [required]

Options:

--help: Show this message and exit.

`primal-page modify add-collection`

Add a Collection to the Collection list in the info.json file

Usage:

$ primal-page modify add-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}

Arguments:

SCHEMEINFO: The path to info.json [required]
COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}: The Collection to add [required]

Options:

--help: Show this message and exit.

`primal-page modify add-link`

Add a link to the selected link field to the info.json

Usage:

$ primal-page modify add-link [OPTIONS] SCHEMEINFO LINKFIELD LINK

Arguments:

SCHEMEINFO: The path to info.json [required]
LINKFIELD: The link field to add to. protocols, validation, homepage, vendors, misc [required]
LINK: The link to add. [required]

Options:

--help: Show this message and exit.

`primal-page modify change-contactinfo`

Change the contactinfo field in the info.json

Usage:

$ primal-page modify change-contactinfo [OPTIONS] SCHEMEINFO CONTACTINFO

Arguments:

SCHEMEINFO: The path to info.json [required]
CONTACTINFO: The contact information for this scheme. Use 'None' to remove the contact info [required]

Options:

--help: Show this message and exit.

`primal-page modify change-derivedfrom`

Replaces the derivedfrom in the info.json file

Usage:

$ primal-page modify change-derivedfrom [OPTIONS] SCHEMEINFO DERIVEDFROM

Arguments:

SCHEMEINFO: The path to info.json [required]
DERIVEDFROM: The new derivedfrom. Use 'None' to remove the derivedfrom [required]

Options:

--help: Show this message and exit.

`primal-page modify change-description`

Replaces the description in the info.json file

Usage:

$ primal-page modify change-description [OPTIONS] SCHEMEINFO DESCRIPTION

Arguments:

SCHEMEINFO: The path to info.json [required]
DESCRIPTION: The new description. Use 'None' to remove the description [required]

Options:

--help: Show this message and exit.

`primal-page modify change-license`

Replaces the license in the info.json file

Usage:

$ primal-page modify change-license [OPTIONS] SCHEMEINFO LICENSE

Arguments:

SCHEMEINFO: The path to info.json [required]
LICENSE: The new license. Use 'None' show the work is not licensed (Not recommended) [required]

Options:

--help: Show this message and exit.

`primal-page modify change-primerclass`

Change the primerclass field in the info.json

Usage:

$ primal-page modify change-primerclass [OPTIONS] SCHEMEINFO PRIMERCLASS:{primerschemes}

Arguments:

SCHEMEINFO: The path to info.json [required]
PRIMERCLASS:{primerschemes}: The primerclass to change to [required]

Options:

--help: Show this message and exit.

`primal-page modify change-status`

Change the status field in the info.json

Usage:

$ primal-page modify change-status [OPTIONS] SCHEMEINFO [SCHEMESTATUS]:[withdrawn|deprecated|autogenerated|draft|tested|validated]

Arguments:

SCHEMEINFO: The path to info.json [required]
[SCHEMESTATUS]:[withdrawn|deprecated|autogenerated|draft|tested|validated]: The scheme class [default: draft]

Options:

--help: Show this message and exit.

`primal-page modify regenerate`

Validates the info.json and regenerate the README.md

Usage:

$ primal-page modify regenerate [OPTIONS] SCHEMEINFO

Arguments:

SCHEMEINFO: The path to info.json [required]

Options:

--help: Show this message and exit.

`primal-page modify remove-author`

Remove an author from the authors list in the info.json file

Usage:

$ primal-page modify remove-author [OPTIONS] SCHEMEINFO AUTHOR

Arguments:

SCHEMEINFO: The path to info.json [required]
AUTHOR: The author to remove [required]

Options:

--help: Show this message and exit.

`primal-page modify remove-citation`

Remove an citation form the authors list in the info.json file

Usage:

$ primal-page modify remove-citation [OPTIONS] SCHEMEINFO CITATION

Arguments:

SCHEMEINFO: The path to info.json [required]
CITATION: The citation to remove [required]

Options:

--help: Show this message and exit.

`primal-page modify remove-collection`

Remove an Collection from the Collection list in the info.json file

Usage:

$ primal-page modify remove-collection [OPTIONS] SCHEMEINFO COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}

Arguments:

SCHEMEINFO: The path to info.json [required]
COLLECTION:{ARTIC|MODJADJI|QUICK-LAB|COMMUNITY|WASTE-WATER|CLINICAL-ISOLATES|WHOLE-GENOME|PANEL|MULTI-TARGET}: The Collection to remove [required]

Options:

--help: Show this message and exit.

`primal-page modify remove-link`

Add a link to the selected link field to the info.json

Usage:

$ primal-page modify remove-link [OPTIONS] SCHEMEINFO LINKFIELD LINK

Arguments:

SCHEMEINFO: The path to info.json [required]
LINKFIELD: The link field to remove from. protocols, validation, homepage, vendors, misc [required]
LINK: The link to remove. [required]

Options:

--help: Show this message and exit.

`primal-page modify reorder-authors`

Reorder the authors in the info.json file

Usage:

$ primal-page modify reorder-authors [OPTIONS] SCHEMEINFO [AUTHOR_INDEX]

Arguments:

SCHEMEINFO: The path to info.json [required]
[AUTHOR_INDEX]: The indexes in the new order, separated by spaces. e.g. 1 0 2. Any indexes not provided will be appended to the end

Options:

--help: Show this message and exit.

`primal-page remove`

Remove a scheme's version from the repo, will also remove size and schemename directories if empty

Usage:

$ primal-page remove [OPTIONS] SCHEMEINFO

Arguments:

SCHEMEINFO: The path to info.json [required]

Options:

--help: Show this message and exit.

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primal-page 1.8.0

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Project links

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Project description

Primal-Page

Contents

Installation

Quick Start

Example

Adding a minimal scheme

Adding a custom scheme to quick-lab/primerschemes

New Schemas

info.json

PrimerNames Versions

V1

V2

ARTIC-primer.bed Versions

V1

V2

V3

Scheme Version

Scheme Name

CLI

primal-page

primal-page aliases

primal-page aliases add

primal-page aliases remove

primal-page build-index

primal-page create

primal-page download

primal-page download all

primal-page download scheme

primal-page modify

primal-page modify add-author

primal-page modify add-citation

primal-page modify add-collection

primal-page modify add-link

primal-page modify change-contactinfo

primal-page modify change-derivedfrom

primal-page modify change-description

primal-page modify change-license

primal-page modify change-primerclass

primal-page modify change-status

primal-page modify regenerate

primal-page modify remove-author

primal-page modify remove-citation

primal-page modify remove-collection

primal-page modify remove-link

primal-page modify reorder-authors

primal-page remove

Project details

Verified details

Maintainers

Unverified details

Project links

Meta

Classifiers

Release history Release notifications | RSS feed

Download files

Source Distribution

Built Distribution

`V1`

`V2`

`primal-page`

`primal-page aliases`

`primal-page aliases add`

`primal-page aliases remove`

`primal-page build-index`

`primal-page create`

`primal-page download`

`primal-page download all`

`primal-page download scheme`

`primal-page modify`

`primal-page modify add-author`

`primal-page modify add-citation`

`primal-page modify add-collection`

`primal-page modify add-link`

`primal-page modify change-contactinfo`

`primal-page modify change-derivedfrom`

`primal-page modify change-description`

`primal-page modify change-license`

`primal-page modify change-primerclass`

`primal-page modify change-status`

`primal-page modify regenerate`

`primal-page modify remove-author`

`primal-page modify remove-citation`

`primal-page modify remove-collection`

`primal-page modify remove-link`

`primal-page modify reorder-authors`

`primal-page remove`