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Description:
primaschema 0.2.0
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
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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