Merge branch '21543-lightning-subdir'

[lightning.git] / manhattan.py

diff --git a/manhattan.py b/manhattan.py
deleted file mode 100644 (file)
index 4736b8a..0000000
--- a/manhattan.py
+++ /dev/null
@@ -1,46 +0,0 @@
-# Copyright (C) The Lightning Authors. All rights reserved.
-#
-# SPDX-License-Identifier: AGPL-3.0
-
-import csv
-import os
-import sys
-
-import matplotlib
-import numpy
-import pandas
-import qmplot
-
-(_,
- input_path,
- output_path,
- ) = sys.argv
-columns = numpy.load(os.path.join(input_path, 'onehot-columns.npy'))
-
-# pvalue maps tag# => [pvalue1, pvalue2, ...] (one het p-value and one hom p-value for each tile variant)
-pvalue = {}
-for i in range(columns.shape[1]):
-    tag = columns[0,i]
-    x = pvalue.get(tag, [])
-    x.append(pow(10, -columns[4,i] / 1000000))
-    pvalue[tag] = x
-
-# tilepos maps tag# => (chromosome, position)
-tilepos = {}
-for dirent in os.scandir(input_path):
-    if dirent.name.endswith('.annotations.csv'):
-        with open(dirent, 'rt', newline='') as annotations:
-            for annotation in csv.reader(annotations):
-                # 500000,0,2,=,chr1,160793649,,,
-                if annotation[3] == "=":
-                    tilepos[int(annotation[0])] = (annotation[4], int(annotation[5]))
-
-series = {"#CHROM": [], "POS": [], "P": []}
-for tag, chrpos in sorted(tilepos.items(), key=lambda item: (item[1][0].lstrip('chr').zfill(2), item[1][1])):
-    for p in pvalue.get(tag, []):
-        series["#CHROM"].append(chrpos[0])
-        series["POS"].append(chrpos[1])
-        series["P"].append(p)
-
-qmplot.manhattanplot(data=pandas.DataFrame(series))
-matplotlib.pyplot.savefig(output_path)