LiGA helper scripts
- Run the MatLab scripts to generate the
AllUniqueFiles
directory - Run the python script
liga_helper
- Python3.x (7, 8 ...) would work for you.
python3 liga_helper.py --all_uniq_dir AllUniqueFiles --barcode_file BarcodeSampleMap.csv --sdb_map_file PhageBarcodeModificationMap.csv --final_output_dir final_output_dir
- Adjust the Rmarkdown file for sample names and meta data and run it.
usage: liga_helper.py [-h] --all_uniq_dir ALL_UNIQ_DIR --barcode_file BARCODE_FILE --sdb_map_file SDB_MAP_FILE --dna_count_table_output_dir DNA_COUNT_TABLE_OUTPUT_DIR
Python script for generating DNA count tables.
optional arguments:
-h, --help show this help message and exit
--all_uniq_dir ALL_UNIQ_DIR
AllUniqueFiles dir
--barcode_file BARCODE_FILE
BarcodeSampleMap.csv
--sdb_map_file SDB_MAP_FILE
PhageBarcodeModificationMap.csv
--dna_count_table_output_dir DNA_COUNT_TABLE_OUTPUT_DIR
DNA count table output directory