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#!/usr/bin/python3
import numpy as np
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt
from ipywidgets.widgets import interact
import interface_utils as util
import sys
import os
os.environ['PATH'] += ':/data/pacbio_assembly/AwesomeAssembler/DALIGNER'
#print os.popen("export").read()
path = os.environ['PWD'] + '/' #/data/pacbio_assembly/AwesomeAssembler/data/'
n = (sys.argv[1])
rst = []
with open(n) as f:
for line in f:
rst.append(int(line.strip()))
rep = {}
with open(path + 'ecoli.repeat.txt') as f:
for line in f:
l = list(map(int, line.strip().split()))
if len(l) > 1:
for i in range((len(l) - 1) / 2):
if l[0] not in rep:
rep[l[0]] = []
rep[l[0]].append((l[2*i+1], l[2*i+2]))
#rst = range(1,1399)
aln = []
for i,e in enumerate(rst):
n = e
print(i,n)
li = list(util.get_alignments_mapping(path+'ecoli', path + 'ecoli.ref', path +'ecoli.ecoli.ref.las', [n]))
if (len(li) > 0):
item = sorted(li, key=lambda x:x[4] - x[3], reverse = True)
for l in item:
aln.append(l)
print(aln[0:20])
#aln.sort(key = lambda x:x[2])
alns = []
current_b = aln[0][2]
aln_group = []
for item in aln:
if current_b != item[2]:
aln_group.sort(key = lambda x:x[4]-x[3], reverse = True)
alns.append(aln_group)
aln_group = []
aln_group.append(item)
current_b = item[2]
else:
aln_group.append(item)
num = len(alns)
print(len(aln), len(alns))
#print [len(item) for item in alns]
#print [item[0:3] for item in aln]
alns.sort(key = lambda x:x[0][3])
#size_chunk = num/grid_size
#for i in range(grid_size):
# aln[i*size_chunk:min((i+1)*size_chunk, num)] = sorted(aln[i*size_chunk:min((i+1)*size_chunk, num)],key = lambda x: x[4]-x[3] ,reverse=True)
plt.figure(figsize = (15,10))
plt.axes()
#plt.gca().axes.get_yaxis().set_visible(False)
l = aln[0][5]
tip = l/5000
ed = l/2000
grid_size = 1.0
plt.xlim(-2000,l+2000)
plt.ylim(-5,num*grid_size)
points = [[0,0], [l,0], [l+tip,grid_size/4], [l,grid_size/2], [0,grid_size/2]]
#rectangle = plt.Rectangle((0, 0), l, 5, fc='r',ec = 'none')
polygon = plt.Polygon(points,fc = 'r', ec = 'none', alpha = 0.6)
plt.gca().add_patch(polygon)
dotted_line = plt.Line2D((0, 0), (0, num*grid_size ),ls='-.')
plt.gca().add_line(dotted_line)
dotted_line2 = plt.Line2D((l, l), (0, num*grid_size ),ls='-.')
plt.gca().add_line(dotted_line2)
for i,aln_group in enumerate(alns):
for item in aln_group:
abpos = item[3]
aepos = item[4]
bbpos = item[6]
bepos = item[7]
blen = item[8]
strand = item[0]
points_start = []
points_end = []
rid = item[2]
abpos = abpos - bbpos
aepos = aepos + (blen - bepos)
if strand == 'n':
points = [[abpos, (i+1)*grid_size], [aepos, (i+1)*grid_size], [aepos + tip, (i+1)*grid_size + grid_size/4], [aepos, (i+1)*grid_size+grid_size/2], [abpos, (i+1)*grid_size+grid_size/2]]
if (bepos < blen):
points_end = [[aepos, (i+1)*grid_size], [aepos + tip, (i+1)*grid_size + grid_size/4], [aepos, (i+1)*grid_size+grid_size/2], [aepos+ed, (i+1)*grid_size+grid_size/2], [aepos + ed+ tip, (i+1)*grid_size + grid_size/4], [aepos+ed, (i+1)*grid_size]]
if (bbpos > 0):
points_start = [[abpos, (i+1)*grid_size], [abpos, (i+1)*grid_size+grid_size/2], [abpos-ed, (i+1)*grid_size+grid_size/2], [abpos-ed, (i+1)*grid_size]]
else:
points = [[abpos, (i+1)*grid_size], [aepos, (i+1)*grid_size], [aepos, (i+1)*grid_size+grid_size/2], [abpos, (i+1)*grid_size+grid_size/2], [abpos - tip, (i+1)*grid_size + grid_size/4]]
if (bepos < blen):
points_end = [[aepos, (i+1)*grid_size], [aepos, (i+1)*grid_size+grid_size/2], [aepos+ed, (i+1)*grid_size+grid_size/2], [aepos+ed, (i+1)*grid_size]]
if (bbpos > 0):
points_start = [[abpos, (i+1)*grid_size],[abpos-tip, (i+1)*grid_size+grid_size/4], [abpos, (i+1)*grid_size+grid_size/2], [abpos-ed, (i+1)*grid_size+grid_size/2],[abpos-ed-tip, (i+1)*grid_size+grid_size/4], [abpos-ed, (i+1)*grid_size]]
polygon = plt.Polygon(points,fc = 'b', ec = 'none', alpha = 0.6)
polygon.set_url("http://shannon.stanford.edu:5000/aln" + str(item[2]+1) + ".pdf")
plt.gca().add_patch(polygon)
#if points_end != []:
# polygon2 = plt.Polygon(points_end,fc = 'g', ec = 'none', alpha = 0.6)
# plt.gca().add_patch(polygon2)
#
#if points_start != []:
# polygon2 = plt.Polygon(points_start,fc = 'g', ec = 'none', alpha = 0.6)
# plt.gca().add_patch(polygon2)
if rid in rep:
for item in rep[rid]:
s = item[0]
e = item[1]
if item[0] == -1:
s = 0
if item[1] == -1:
e = blen
if strand != 'n':
s = blen - s
e = blen - e
points = [[abpos + s, (i+1)*grid_size], [abpos + e, (i+1)*grid_size], [abpos + e, (i+1)*grid_size+grid_size/2], [abpos + s, (i+1)*grid_size+grid_size/2]]
polygon2 = plt.Polygon(points,fc = 'y', ec = 'none', alpha = 0.8)
plt.gca().add_patch(polygon2)
plt.savefig('mapping/map.svg')
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