#!/usr/bin/env python3
"""
Purpose
-------
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
:py:func:`main` executor.
- ``mash_output`` : String with the name of the mash screen output file.
- e.g.: ``'fastaFileA_mashdist.txt'``
Code documentation
------------------
"""
__version__ = "1.1.1"
__build__ = "03042018"
__template__ = "mashsdist2json-nf"
import os
import json
from assemblerflow_utils.assemblerflow_base import get_logger, MainWrapper
logger = get_logger(__file__)
if __file__.endswith(".command.sh"):
MASH_TXT = '$mashtxt'
HASH_CUTOFF = '$params.shared_hashes'
logger.debug("Running {} with parameters:".format(
os.path.basename(__file__)))
logger.debug("MASH_TXT: {}".format(MASH_TXT))
logger.debug("HASH_CUTOFF: {}".format(HASH_CUTOFF))
[docs]def send_to_output(master_dict, last_seq, mash_output):
"""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
Parameters
----------
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.
Returns
-------
"""
# create a new file only if master_dict is populated
if master_dict:
out_file = open("{}_{}.json".format(
"".join(mash_output.split(".")[0]), last_seq), "w")
out_file.write(json.dumps(master_dict))
out_file.close()
@MainWrapper
def main(mash_output, hash_cutoff):
'''
Main function that allows to dump a mash dist txt file to a json file
Parameters
----------
mash_output: str
A string with the input file.
'''
# out_file = open(".".join(mash_output.split(".")[:-1]) + ".json", "w")
input_f = open(mash_output, "r")
master_dict = {}
# used to store the last sequence to be parsed (useful for multifasta)
last_seq = ""
counter = 0
for line in input_f:
tab_split = line.split("\t")
current_seq = tab_split[1].strip()
ref_accession = "_".join(tab_split[0].strip().split("_")[0:3])
mash_dist = tab_split[2].strip()
hashes_list = tab_split[-1].strip().split("/")
# creates a percentage of the shared hashes between the sample and the
# reference
perc_hashes = float(hashes_list[0]) / float(hashes_list[1])
# assures that only the hashes with a given shared percentage are
# reported to json file
if perc_hashes > float(hash_cutoff):
if last_seq != current_seq and counter > 0:
# create a new file only if master_dict is populated
send_to_output(master_dict, last_seq, mash_output)
master_dict = {}
counter = 0
# if counter = 0 last_seq should be updated before the next if statement
if counter == 0:
counter += 1
last_seq = current_seq
# then if last_seq is equal to current_seq write to dict
if last_seq == current_seq:
master_dict[ref_accession] = [1 - float(mash_dist), perc_hashes]
last_seq = current_seq
# assures that file is closed in last iteration of the loop
send_to_output(master_dict, last_seq, mash_output)
if __name__ == "__main__":
main(MASH_TXT, HASH_CUTOFF)