create_manifest.md

Detailed documentation for create_manifest.py

Optional step between [1/7] and [2/7] of the prediction pipeline creates a keyfile that coordinates processing multiple contigs at the same time.

python create_manifest.py \
--input-zarr path/to/output/sequence.zarr \
--output-json path/to/output/manifest.json \
--species-id species_name \
--intermediate-dir path/to/output

Parameters

• --input-zarr -i- - sequences.zarr file from extract_fasta.py
• --output-json -o - output manifest.json file
• --species-id - The name of the species or sample
• --intermediate-dir- Path to a directory which will store intermediate GeneCAD files. By default, this is the parent directory of input-zarr

Manifest Format

GeneCAD manifest files use human-readable JSON format to list the parameters specific to each chromosome while using the prediction pipeline. The following parameters are required:

• chromosome_id - name of the chromosome
• sequence_zarr - sequences.zarr file from extract_fasta.py
• predictions_dir - predictions directory from predict.py
• intervals_zarr - intervals.zarr file from detect_intervals.py
• raw_gff - unfiltered gff file from export_gff.py
• filtered_gff - post-filter gff file from filter_raw_gff.py

An example of the formatting for the manifest file

[{"chromosome_id": "Chr1", "sequence_zarr": "sequence.zarr", "predictions_dir": "predictions_Chr1/", "intervals_zarr": "intervals_Chr1.zarr", "raw_gff": "predictions_raw_Chr1.gff", "filtered_gff": "predictions_filtered_Chr1.gff"},
{"chromosome_id": "Chr2", "sequence_zarr": "sequence.zarr", "predictions_dir":"predictions_Chr2/", "intervals_zarr": "intervals_Chr2.zarr", "raw_gff": "predictions_raw_Chr2.gff", "filtered_gff": "predictions_filtered_Chr2.gff"},
{"chromosome_id": "Chr3", "sequence_zarr": "sequence.zarr", "predictions_dir":"predictions_Chr3/", "intervals_zarr": "intervals_Chr3.zarr", "raw_gff": "predictions_raw_Chr3.gff", "filtered_gff": "predictions_filtered_Chr3.gff"}]

Next Step

python predict.py Predict Documentation