aln2type

Use variant_definitions to type an MSA of SARS-CoV-2 sequences, handling insertions.

MSA must include MN908947.3 to correctly label variant positions.

Install

git clone https://github.com/connor-lab/aln2type

cd aln2type

pip install .

git clone https://github.com/phe-genomics/variant_definitions

Help

usage: aln2type [-h] [--csv_N] [--no_gzip_json] [--output_unclassified]
                [--no_call_deletion] [--gb GB]
                json_outdir sample_csv_outdir summary_csv_outfile ref_name msa
                typing_yaml [typing_yaml ...]

positional arguments:
  json_outdir           Output directory for typing JSON
  sample_csv_outdir     Output directory for sample variant CSVs
  summary_csv_outfile   Output summary CSV file
  ref_name              Name of reference sequence in MSA
  msa                   Path to MSA
  typing_yaml           Path to Variant definition YAML files

optional arguments:
  -h, --help            show this help message and exit
  --csv_N               Include Ns in sample variant CSVs
  --no_trim_terminal_N  Don't trim Ns from sequence terminus. Default behaviour is to trim Ns and gaps BEFORE analysis
  --no_gzip_json        Don't gzip typing JSON files
  --output_unclassified
                        Retain unclassified samples in summary CSV
  --no_call_deletion    Allow deleted positions to be treated as no-calls not
                        ref
  --gb GB               Path to annotation GenBank

Run

aln2type sample_json_out sample_csv_out typing_summary.csv MN908947.3 sars_cov_2.aln variant_definitions/variant_yaml/*.yml