flowcraft.templates.mashdist2json module


This module is intended to generate a json output for mash dist results that can be imported in pATLAS.

Expected input

The following variables are expected whether using NextFlow or the main() executor.

  • mash_output : String with the name of the mash screen output file.
    • e.g.: 'fastaFileA_mashdist.txt'

Code documentation

flowcraft.templates.mashdist2json.send_to_output(master_dict, mash_output, sample_id, assembly_file)[source]

Send dictionary to output json file This function sends master_dict dictionary to a json file if master_dict is populated with entries, otherwise it won’t create the file

master_dict: dict

dictionary that stores all entries for a specific query sequence in multi-fasta given to mash dist as input against patlas database

last_seq: str

string that stores the last sequence that was parsed before writing to file and therefore after the change of query sequence between different rows on the input file

mash_output: str

the name/path of input file to main function, i.e., the name/path of the mash dist output txt file.

sample_id: str

The name of the sample being parse to .report.json file