Create JSON files with count data to be browsed in GEAR/HALO

Snakefile

@@ -77,6 +77,10 @@ rule all:
                bpdens = ["selected"],
                method = METHODS,
                plottype = ["byaf","bypos"]),
+        expand("halo/{sample}/{window}_{suffix}.json.gz",
+               sample = SAMPLES,
+               window = [100000],
+               suffix = ["fixed", "fixed_norm"])
 
 
 ################################################################################
@@ -299,6 +303,17 @@ rule plot_SV_consistency_barplot:
         "utils/sv_consistency_barplot.snakemake.R"
 
 
+rule generate_halo_json:
+    input:
+        counts = "counts/{sample}/{windows}.txt.gz",
+    output:
+        json = "halo/{sample}/{windows}.json.gz",
+    log:
+        "log/generate_halo_json/{sample}/{windows}.{windows}.log"
+    shell:
+        "(./utils/counts_to_json.py {input.counts} | gzip > {output.json}) 2> {log}"
+
+
 ################################################################################
 # Read counting                                                                #
 ################################################################################

utils/counts_to_json.py

+#!/usr/bin/env python
+
+import sys
+from argparse import ArgumentParser
+import gzip
+import json
+from collections import defaultdict, namedtuple
+
+class CountTable:
+	def __init__(self, filename):
+		# maps (cell,chromosome) to a list of counts (start, end, w, c)
+		self.counts = defaultdict(list)
+		for i, line in enumerate(gzip.open(filename)):
+			if i == 0:
+				fieldnames = list(x.decode() + '_' for x in line.split())
+				Fields = namedtuple('Fields', fieldnames)
+			else:
+				f = list(x.decode() for x in line.split())
+				fields = Fields(*f)
+				self.counts[(fields.cell_,fields.chrom_)].append(
+					(int(fields.start_),int(fields.end_),float(fields.w_),float(fields.c_))
+				)
+
+
+	def write_json(self):
+		cells = sorted(set(cell for (cell,chromosome) in self.counts.keys()))
+		chromosomes = sorted(set(chromosome for (cell,chromosome) in self.counts.keys()))
+		# list of dicts (one per cell) to be serialized as JSON
+		l = []
+		for cell in cells:
+			d_cell = {}
+			d_cell["sample"] = cell
+			d_cell["coverages"] = [
+				{
+					"chromosome": chromosome,
+					"positions": [start for (start, end, w, c) in self.counts[(cell,chromosome)]],
+					"counts": [
+						{
+							"label": "Watson", 
+							"values": [w for (start, end, w, c) in self.counts[(cell,chromosome)]]
+						},
+						{
+							"label": "Crick", 
+							"values": [c for (start, end, w, c) in self.counts[(cell,chromosome)]]
+						},
+					]
+				} for chromosome in chromosomes
+			]
+			l.append(d_cell)
+		json.dump({"data": l}, sys.stdout)
+
+def main():
+	parser = ArgumentParser(prog='counts_to_json.py', description=__doc__)
+	parser.add_argument('counts', metavar='COUNT', help='Gzipped, tab-separated table with counts')
+	args = parser.parse_args()
+
+	print('Reading count table from', args.counts, file=sys.stderr)
+	count_table = CountTable(args.counts)
+	print(' ... done.', file=sys.stderr)
+
+	count_table.write_json()
+
+
+if __name__ == '__main__':
+	main()