def generateContactPlots(links_file,
bin_length,
chrom_file=wsn_chroms,
dir='.',
prefix='',
make_binned_file=True,
use_log_scale=False,
cross_segment_intensities=False):
plot_dir = jpk_util.getDir(dir + '/contact_plots')
link_dir = jpk_util.getDir(dir + '/links')
# dictionary of segments & the start coordinate of each of their buckets
seg_lens = jpk_util.getChromSizes(chrom_file)
bin_dict = {}
for segment in seg_lens:
bin_dict[segment] = getChromBins(seg_lens[segment], bin_length)
# Create bin matrices
link_matrix = getBinnedLinkMatrix(links_file, bin_dict, seg_lens)
if make_binned_file:
makeBinnedFile(link_matrix, bin_length, dir=link_dir, prefix=prefix)
drawContactPlots(link_matrix,
chrom_file,
dir=plot_dir,
prefix=prefix,
use_log_scale=use_log_scale,
cross_segment_intensities=cross_segment_intensities)
return link_matrix
def makeInteractionFiles(link_file,
dir='.',
prefix='',
chrom_size_file=wsn_chroms,
fromJuncs=True):
'''
Generates all three files used for Circos
'''
dir = jpk_util.getDir(dir)
try:
if (fromJuncs):
junc_file = makeJunctionSiteFile(link_file, dir=dir, prefix=prefix)
bg = makeBedgraphFromLinks(junc_file,
dir=dir,
prefix=prefix,
chrom_size_file=chrom_size_file)
return (junc_file, bg)
else:
bg = makeBedgraphFromLinks(link_file,
dir=dir,
prefix=prefix,
chrom_size_file=chrom_size_file)
return (None, bg)
except Exception as e:
raise e
exit(2)
def makeJunctionSiteFile(link_file,
dir='.',
prefix='',
out_name='',
num_nt_from_junc=10):
'''
Creates a link file of positions 10 nucleotides into the read from
the junction sites. So if the link file says:
PA 10 50 NA 7 30
Then the junction file will say:
PA 40 50 NA 7 17
'''
dir = jpk_util.getDir(dir)
junc_file = dir + '/' + prefix + '_inter_junctions.links'
if (out_name != ''):
junc_file = dir + '/' + out_name
f_out = open(junc_file, 'w+')
for line in open(link_file, 'r'):
fields = line.split()
if len(fields) < 6:
continue
seg1, st1, end1, seg2, st2, end2 = fields[0:6]
if seg1 != seg2: # only look at intersegmental junctions
st1_upd = str(int(end1) - num_nt_from_junc)
end2_upd = str(int(st2) + num_nt_from_junc)
out_line = '\t'.join([seg1, st1_upd, end1, seg2, st2, end2_upd])
if len(fields) > 6: # add circos color if it's there
out_line += '\t' + fields[6]
print(out_line, file=f_out)
f_out.close()
return junc_file
def makeBedgraphFromLinks(link_file,
dir='.',
prefix='',
out_name='',
chrom_size_file=wsn_chroms):
'''
Generate a bedgraph from the links. This can act as a histogram for
the interactions that can be added to the border of the Circos plot
'''
dir = jpk_util.getDir(dir)
bedgraph = dir + '/' + prefix + '_inter.bedgraph'
if (out_name != ''):
bedgraph = dir + '/' + out_name
# This awk cmd will split the links into two separate lines, so:
# PA 10 100 NA 20 30
# Will become:
# PA 10 100
# NA 20 30
awk_cmd = '\'{print $1\"\\t\"$2\"\\t\"$3\"\\n\"$4\"\\t\"$5\"\\t\"$6}\''
# To leverage genomeCoverageBed, need to use system commands
pipeline = ' '.join([
'awk', awk_cmd, link_file, '|', 'sort', '-k1,1', '-k2,2n', '|',
'genomeCoverageBed', '-bga', '-i', 'stdin', '-g', chrom_size_file, '>',
bedgraph
])
os.system(pipeline)
return bedgraph
def generateThresholdLinks(inter_links_file,
threshold=3,
window=20,
dir='.',
prefix='',
chroms_size_file=wsn_chroms,
out_file=''):
seg_lens = jpk_util.getChromSizes(chroms_size_file)
bin_dict = {}
for segment in seg_lens:
bin_dict[segment] = cp.getChromBins(seg_lens[segment], window)
new_dir = jpk_util.getDir(dir)
if dir == '.':
new_dir = (new_dir + '/binned_' + str(window) + '_junc_sites_t' +
str(threshold))
link_matrix = cp.getBinnedLinkMatrix(inter_links_file,
bin_dict,
seg_lens,
just_inter=True,
include_nojuncs=False)
binned_thresh_file = (new_dir + '/' + prefix + '_binned_' + str(window) +
'_ge' + str(threshold) + '_links.txt')
if out_file != '':
binned_thresh_file = out_file
f_out = open(binned_thresh_file, 'w+')
for link in link_matrix:
if link_matrix[link] >= threshold:
tup1, tup2 = link.split('-')
seg1, bin1 = tup1.split(':')
next_bin = int(bin1) + 1
end1 = seg_lens[seg1]
if len(bin_dict[seg1]) > next_bin:
end1 = bin_dict[seg1][next_bin] - 1
st1 = bin_dict[seg1][int(bin1)]
seg2, bin2 = tup2.split(':')
next_bin = int(bin2) + 1
end2 = seg_lens[seg2]
if len(bin_dict[seg2]) > next_bin:
end2 = bin_dict[seg2][next_bin] - 1
st2 = bin_dict[seg2][int(bin2)]
out_line = '\t'.join(
[seg1, str(st1),
str(end1), seg2,
str(st2),
str(end2)])
print(out_line, file=f_out)
f_out.close()
return binned_thresh_file
def makeBinnedFile(link_matrix, bin_len, dir='.', prefix=''):
bins_with_vals = [(x, link_matrix[x]) for x in link_matrix
if link_matrix[x] > 0]
dir = jpk_util.getDir(dir)
binned_links_file = (dir + '/' + prefix + '_binned_' + str(bin_len) +
'_links.txt')
out_f = open(binned_links_file, 'w+')
for bin, numLinks in bins_with_vals:
print(bin + "\t" + str(numLinks), file=out_f)
out_f.close()
def makeIntersegFile(link_file, dir='.', prefix='', out_name=''):
'''
Creates a link file of just intersegmental ineractions
'''
dir = jpk_util.getDir(dir)
interseg_file = dir + '/' + prefix + '_inter.links'
if (out_name != ''):
interseg_file = dir + '/' + out_name
awk_cmd = 'awk \'$1!=$4\' ' + link_file + ' > ' + interseg_file
os.system(awk_cmd)
return interseg_file
def generateSashimi(links_file, dir='.', prefix=''):
'''
links_file should be the output from makeLinkFile
dir is the output directory
prefix is the prefix for the sashimi bed file
'''
dir = jpk_util.getDir(dir)
sashimi_bed = dir + '/' + prefix + '_sashimi.bed'
f1 = open(links_file, 'r')
f2 = open(sashimi_bed, 'w+')
# This will allow IGV to interpret the file as junctions
f2.write('track name=%s_junctions or graphType=junctions\n' % prefix)
for line in f1:
ln = line.strip().split()
if (len(ln) < 6):
continue
seg1 = ln[0]
start1 = int(ln[1])
end1 = int(ln[2])
seg2 = ln[3]
start2 = int(ln[4])
end2 = int(ln[5])
intra_segmental = seg1 == seg2
more_than_3_nt = abs(start1 - start2) > 3
non_overlapping = ((start1 < start2 or start1 > end2)
and (start2 < start1 or start2 > end1))
if intra_segmental and more_than_3_nt and non_overlapping:
s1 = min(start1, start2)
s2 = max(start1, start2)
e1 = min(end1, end2)
e2 = max(end1, end2)
f2.write(
('{}\t{}\t{}\t.\t1\t-\t{}\t{}\t150,50' +
',50,30\t2\t{},{}\t0,{}\n').format(seg1, s1, e2, s1, e2,
e1 - s1, e2 - s2, s2 - s1))
f1.close()
f2.close()
def runCircosFromLinks(links_file,
dir='.',
prefix='',
chrom_size_file=wsn_chroms,
colored=False,
hitsclip_bg_path=None,
include_hist=True,
ribbon=False,
fromJuncs=True):
dir = jpk_util.getDir(dir)
circos_dir = dir + '/circos'
conf_dir = dir + '/circos/conf'
juncs, bg = makeInteractionFiles(links_file,
dir=circos_dir,
prefix=prefix,
chrom_size_file=chrom_size_file,
fromJuncs=fromJuncs)
if not include_hist:
bg = None
conf_file = makeCircosConf(links_file,
prefix=prefix,
dir=conf_dir,
hitsclip_bg_path=hitsclip_bg_path,
hist_path=bg,
ribbon=ribbon,
colored=colored)
pipeline = ' '.join([
'circos', '-conf', conf_file, '-outputdir', circos_dir, '-outputfile',
prefix + '_circos'
])
os.system(pipeline)
def main():
try:
opts, args = getopt.getopt(sys.argv[1:], 'hCSUxclvi:o:p:s:Hg:b:')
except getopt.GetoptError:
displayUsage()
sys.exit(2)
doCircos = False
doSashimi = False
doContact = False
junction_file = ''
prefix = ''
output = '.'
chrom_size_file = wsn_chroms
hits_clip_file = None
bin_size = DEFAULT_BIN_SIZE
use_log_scale = False
colored = False
include_hist = True
cross_segment_intensities = False
for opt, arg in opts:
if opt == '-h':
displayUsage()
sys.exit()
elif opt == "-i":
junction_file = arg
elif opt == "-o":
output = arg
elif opt == "-p":
prefix = arg
elif opt == "-v":
verbose = True
elif opt == "-c":
colored = True
elif opt == "-s":
chrom_size_file = arg
elif opt == '-H':
include_hist = False
elif opt == '-g':
hits_clip_file = arg
elif opt == '-b':
bin_size = int(arg)
elif opt == '-l':
use_log_scale = True
elif opt == '-x':
cross_segment_intensities = True
elif opt == '-C':
doCircos = True
elif opt == '-S':
doSashimi = True
elif opt == '-U':
doContact = True
chrom_size_file = jpk_util.getDir(chrom_size_file)
if junction_file == '':
displayUsage()
sys.exit(2)
if prefix == '':
prefix = os.path.basename(junction_file)
prefix = prefix[0:prefix.index('.')]
links_dir = output + '/links'
link_file = jpk_util.makeLinkFile(junction_file,
dir=links_dir,
prefix=prefix)
if doCircos:
inter_links = circos.makeIntersegFile(link_file,
dir=output + '/circos',
prefix=prefix)
circos.runCircosFromLinks(inter_links,
dir=output,
prefix=prefix,
chrom_size_file=chrom_size_file,
colored=colored,
hitsclip_bg_path=hits_clip_file,
include_hist=include_hist)
if doSashimi:
sashimi.generateSashimi(link_file,
dir=output + '/sashimi',
prefix=prefix)
if doContact:
contactPlots.generateContactPlots(
link_file,
bin_size,
chrom_file=chrom_size_file,
dir=output,
prefix=prefix,
use_log_scale=use_log_scale,
cross_segment_intensities=cross_segment_intensities)
import sys
import time
import re
import pandas as pd
import matplotlib.pyplot as plt
import subprocess
import math
import numpy as np
import scipy
import jpk_util
from matplotlib import figure
from PIL import Image
from PIL import ImageChops
from subprocess import call
wsn_chroms = jpk_util.getDir('../genome/WSN/WSN.chrom.sizes')
# Path used for annotation of the upper triangle plots
SEGMENT_AXES = ('/Users/jpk90/Desktop/scripts/python/img/segment_axes')
def getChromBins(chrom_len, bin_len):
if bin_len > chrom_len:
return [0]
num_windows = int(chrom_len / bin_len)
leftover_chrom = int(chrom_len % num_windows / 2)
bins = [(leftover_chrom) + bin_len * i for i in range(1, num_windows)]
bins = [0] + bins
return bins
def makeCircosConf(inter_links,
prefix='',
dir='.',
colored=False,
hitsclip_bg_path=None,
hist_path=None,
use_redux=True,
out_name='',
ribbon=False):
'''
colored defines whether the junctions will be colored or not. Nara
has mentioned that it is probably more useful if it's not colored,
since
hitsclip_bg_path is an optional parameter to include a bedgraph of
HITS-CLIP data which will be seen around the plot
'''
dir = jpk_util.getDir(dir)
if not colored:
need_new_link_file = False
for line in open(inter_links, 'r'):
if len(line.strip().split()) > 6:
need_new_link_file = True
break
if need_new_link_file:
bname = '.'.join(os.path.basename(inter_links).split('.')[0:-1])
new_link_file = inter_links.replace(bname, bname + '_nocolor')
f_out = open(new_link_file, 'w+')
for line in open(inter_links, 'r'):
fields = line.strip().split()
if len(fields) >= 6:
print('\t'.join(fields[0:6]), file=f_out)
inter_links = new_link_file
f_out.close()
template = ''
out_circos_name = dir + '/' + prefix + '.conf'
template = conf_template
f_in = open(template, 'r')
f_out = open(out_circos_name, 'w+')
for line in f_in:
ln = line.strip().split()
if len(ln) > 0 and ln[0] == 'links_file':
f_out.write('links_file = ' + inter_links + '\n')
elif len(ln) > 0 and ln[0] == 'hist_file' and hist_path:
f_out.write('hist_file = ' + hist_path + '\n')
elif len(ln) > 0 and ln[0] == 'hits_clip_file' and hitsclip_bg_path:
f_out.write('hits_clip_file = ' + hitsclip_bg_path + '\n')
elif len(ln) > 0 and ln[0] == 'ribbon':
if ribbon:
f_out.write('ribbon = yes\n')
else:
f_out.write('ribbon = no\n')
elif len(ln) > 0 and ln[0] == 'karyotype':
f_out.write('karyotype = ' + influenza_karyotype + '\n')
else:
f_out.write(line)
f_in.close()
f_out.close()
return out_circos_name
import os
import sys
import subprocess
import jpk_util
import contactPlots as cp
from subprocess import call
# Circos template configuration path
conf_template = jpk_util.getDir('../plots_lib/circos/template.conf')
influenza_karyotype = jpk_util.getDir(
'../plots_lib/circos/influenza_karyotype.txt')
wsn_chroms = jpk_util.getDir('../genome/WSN/WSN.chrom.sizes')
def makeIntersegFile(link_file, dir='.', prefix='', out_name=''):
'''
Creates a link file of just intersegmental ineractions
'''
dir = jpk_util.getDir(dir)
interseg_file = dir + '/' + prefix + '_inter.links'
if (out_name != ''):
interseg_file = dir + '/' + out_name
awk_cmd = 'awk \'$1!=$4\' ' + link_file + ' > ' + interseg_file
os.system(awk_cmd)
return interseg_file
def makeJunctionSiteFile(link_file,
dir='.',
prefix='',