#! /usr/bin/env python

"""

Script that takes a ST-data file in JSON

format from the ST Pipeline and converts it

to a data frame (genes as columns and spots as rows).

The JSON format must be like this :

[

{

"y": 25,

"x": 31,

"hits": 1,

"barcode": "GATCGCTGAAAGGATAGA",

"gene": "ENSMUSG00000041378"

},

{

"y": 23,

"x": 13,

"hits": 4,

"barcode": "TGTTCCGATGGGAGAAGC",

"gene": "ENSMUSG00000001227"

},

....

The output data frame will be like

gene gene ...

XxY count count

XxY count count

...

@Author Jose Fernandez Navarro <jose.fernandez.navarro@scilifelab.se>

"""

import argparse

import sys

import os

from collections import defaultdict

import pandas as pd

import json

def main(json_file, outfile):

if not os.path.isfile(json_file) or not json_file.endswith(".json"):

sys.stderr.write("Error, input file not present or invalid format\n")

sys.exit(1)

if not outfile:

outfile = "data_table.tsv"

# Iterate the JSON file to get the counts

genes_spot_counts = defaultdict(lambda : defaultdict(int))

with open(json_file, "r") as fh:

for line in json.load(fh):

gene = line["gene"]

x = line["x"]

y = line["y"]

count = line["hits"]

spot = "{0}x{1}".format(x, y)

genes_spot_counts[spot][gene] = count

# Obtain a list of the row names (indexes)

# and list of list of gene->count for the columns (of each row)

list_row_values = list()

list_indexes = list()

for key,value in genes_spot_counts.iteritems():

list_indexes.append(key)

list_row_values.append(value)

# Create a data frame (genes as columns, spots as rows)

counts_table = pd.DataFrame(list_row_values, index=list_indexes)

# Write table to a file

counts_table.to_csv(outfile, sep="\t", na_rep=0)

if __name__ == '__main__':

parser = argparse.ArgumentParser(description=__doc__,

formatter_class=argparse.RawDescriptionHelpFormatter)

parser.add_argument("--json-file", required=True,

help="ST data file in JSON format")

parser.add_argument("--outfile", default=None, help="Name of the output file")

args = parser.parse_args()

main(args.json_file, args.outfile)