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32_accessible_regions_pic.py
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#!/usr/bin/python3
#
# This file is part of Progesterone pipeline.
#
# Progesterone pipeline is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Progesterone pipeline is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with Progesterone pipeline. If not, see <https://www.gnu.org/licenses/>.
#
from utils.mysqldb import *
from utils.utils import *
from math import log
import matplotlib.pyplot as plt
import numpy as np
def rescaled (x, offset, scale):
return (x-offset)/scale
def atac_points(db, cursor, assembly, chromosome, tad_start, tad_end, tad_length):
points = []
values = []
weights = []
qry = "select r.rfrom, r.rto, a. logfold_change, a.pval from regions as r, atac_acc_changes as a "
qry += "where r.assembly='%s' and r.chromosome='%s' " % (assembly, chromosome)
qry += "and r.rtype='atacseq' and r.rfrom>=%d and r.rto<=%d " % (tad_start, tad_end)
qry += "and a.atac_region_id=r.id"
ret = search_db(cursor,qry)
hard_check (db, cursor, ret, qry)
for line in ret:
[start, end, logfold_change, pval] = line
start = int(start)
end = int(end)
if end<tad_start: continue
if start>tad_end: continue
midpoint = (start+end)/2
point_rescaled = rescaled(midpoint, tad_start, tad_length)
if pval==0:
weight = 5
else:
weight = -log(float(pval))
points.append(point_rescaled)
values.append(float(logfold_change))
weights.append(weight)
sorted_indices = [i for i in range(len(points))]
sorted_indices.sort(key=lambda i: points[i])
np_points = np.array(points)[sorted_indices]
np_values = np.array(values)[sorted_indices]
np_weights = np.array(weights)[sorted_indices]
#for i in range(np_points.size):
# print("%.3f %5.1f %1.f" % (np_points[i], np_values[i], np_weights[i]))
return np_points, np_values, np_weights
#########################################
def main():
assembly = "hg19"
gene_name = "Hand2"
tad_external_exp_id = "ENCFF633ORE"
atac_pubmed_id = "29259032"
conf_file = "/home/ivana/.mysql_conf"
for prerequisite in [conf_file]:
if os.path.exists(prerequisite): continue
print(prerequisite, "not found")
exit()
######################################
db = connect_to_mysql(conf_file)
cursor = db.cursor()
switch_to_db(cursor,'progesterone')
atac_xref_id = store_xref (cursor, 'pubmed', atac_pubmed_id)
tad_xref_id = get_xref_id(db,cursor,tad_external_exp_id)
# find gene coordinates
[chromosome, strand, gene_start, gene_end] = get_gene_coords(db,cursor,gene_name,assembly)
# tad?
[tad_start, tad_end] = get_tad_region(db, cursor, tad_xref_id, chromosome, gene_start, gene_end)
tad_length = tad_end - tad_start
# binding regions
chipseq_regions_ESR1 = get_binding_regions_in_interval(db, cursor, assembly, chromosome, tad_start, tad_end, 'ESR1')
chipseq_regions_PGR = get_binding_regions_in_interval(db, cursor, assembly, chromosome, tad_start, tad_end, 'PGR')
# atacseq regions (np_ are numpy arrays)
np_atac_points, np_atac_values, np_atac_weights = atac_points(db, cursor, assembly, chromosome, tad_start, tad_end, tad_length)
cursor.close()
db.close()
######################################
colors = []
maxw = np.amax(np_atac_weights)
for w in np_atac_weights:
colors.append((0.29,0,0.5, w/maxw))
fig, ax = plt.subplots()
ax.axhline(0, color='black', lw=1)
#ax.plot(np_points, np_values, 'o')
plt.bar(np_atac_points, np_atac_values, width=0.01, color=colors)
hand2_start = rescaled(gene_start, tad_start, tad_length)
hand2_end = rescaled(gene_end, tad_start, tad_length)
ax.hlines(y=0.0, xmin=hand2_start-0.002, xmax=hand2_end+0.002, linewidth=30, color='b')
for chipseq_reg in chipseq_regions_ESR1:
[start, end] = [rescaled(int(p), tad_start, tad_length) for p in chipseq_reg]
ax.hlines(y=0.0, xmin=start-0.002, xmax=end+0.002, linewidth=30, color='r')
for chipseq_reg in chipseq_regions_PGR:
[start, end] = [rescaled(int(p), tad_start, tad_length) for p in chipseq_reg]
ax.hlines(y=0.0, xmin=start-0.002, xmax=end+0.002, linewidth=30, color='g')
plt.show()
return
#########################################
if __name__== '__main__':
main()