primaschema 0.2.0

A toolkit for primer scheme defintions

Primaschema

The toolkit for validating and building tiling amplicon PCR primer scheme definitions for inclusion in the PHA4GE primer-schemes repository, starting from either 6 or 7 column Primal Scheme-like BED files and metadata contained in a YAML file.

Install (Python 3.10+)

git clone https://github.com/pha4ge/primaschema
pip install primer-schemes

Some primaschema commands use components from the primer-schemes repository. To show Primaschema where to find these, create the evironment variable PRIMER_SCHEMES_PATH pointing to the location of the primer-schemes directory on your machine:

git clone https://github.com/pha4ge/primer-schemes.git
export PRIMER_SCHEMES_PATH="/path/to/primer-schemes"

Usage

% primaschema --help
usage: primaschema [-h] [--version]
                   {hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts}
                   ...

positional arguments:
  {hash-ref,hash-bed,validate,validate-recursive,build,build-recursive,build-manifest,diff,6to7,7to6,show-non-ref-alts}
    hash-ref            Generate reference sequence checksum
    hash-bed            Generate a bed file checksum
    validate            Validate a primer scheme bundle containing info.yml, primer.bed and reference.fasta
    validate-recursive  Recursively validate primer scheme bundles in the specified directory
    build               Build a primer scheme bundle containing info.yml, primer.bed and reference.fasta
    build-recursive     Recursively build primer scheme bundles in the specified directory
    build-manifest      Build a complete manifest of schemes contained in the specified directory
    diff                Show the symmetric difference of records in two bed files
    6to7                Convert a 6 column scheme.bed file to a 7 column primer.bed file using a reference sequence
    7to6                Convert a 7 column primer.bed file to a 6 column scheme.bed file by droppign a column
    show-non-ref-alts   Show primer records with sequences not matching the reference sequence

options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit


% primaschema build test/data/primer-schemes/eden/v1
INFO: Scheme bed file has the expected number of columns (6)
INFO: Writing info.yml with checksums
INFO: Generating primer.bed from scheme.bed and reference.fasta

info.yml example

schema_version: 1-0-0
name: eden-v1
organism: SARS-CoV-2
organism_aliases:
  - nCoV-2019
aliases:
  - sydney
developers:
  - name: John-Sebastian Eden
    url: https://orcid.org/0000-0003-1374-3551
  - name: Eby Sim
    url: https://orcid.org/0000-0002-3716-7344
vendors: []
amplicon_size: 2500
repository_url: https://github.com/pha4ge/primer-schemes/tree/main/sars-cov-2/eden/v1
citations:
  - https://www.protocols.io/view/sars-cov-2-genome-sequencing-using-long-pooled-amp-kxygxeob4v8j/v1
notes:
  - Protocol includes addendum for ONT sequencing
primer_checksum: "primaschema:9e4c6a3b84cbd76cb3e38b893d0322b5799ecafe28d8cf7bf347ce6dcc5ee8cb"
reference_checksum: "primaschema:7d5621cd3b3e498d0c27fcca9d3d3c5168c7f3d3f9776f3005c7011bd90068ca"

Development

# Inside a clean Python 3.10+ environment
git clone https://github.com/pha4ge/primaschema.git
cd primaschema
pip install --editable ./
pytest