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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'] += ':~/AwesomeAssembler/DALIGNER'
#print os.popen("export").read()
left = int(sys.argv[1])
right = int(sys.argv[2])
ref = sys.argv[3]
read = sys.argv[4]
las = sys.argv[5]
contig = sys.argv[6]
length_th = int(sys.argv[7])
#path = '/data/pacbio_assembly/AwesomeAssembler/data/ecoli/'
aln = []
#bb = []
#with open('ecoli.linear.edges') as f:
# for line in f:
# e = line.split(" ")[0]
# if e[-1] == '\'':
# e = e[:-1]
#
# bb.append(int(e))
#
#print bb
#
#bb = set(bb)
for i,item in enumerate(util.get_alignments_mapping3(ref, read, las, contig)):
if i%2000 == 0:
print(i, item)
if item[3] >= left and item[4] <= right and item[4] - item[3] > length_th:
aln.append(item)
covy = np.zeros((right - left, ))
for item in aln:
covy[item[3] - left : item[4] - left] += 1
covx = np.arange(left, right)
print('number:',len(aln))
aln.sort(key = lambda x:x[2])
alns = []
current_b = aln[0][2]
aln_group = []
for item in aln:
if current_b != item[2]:
alns.append(aln_group)
aln_group = []
aln_group.append(item)
current_b = item[2]
else:
aln_group.append(item)
#num = len(alns)
num = len(aln)
print(len(aln), len(alns))
alns.sort(key = lambda x:min([item[3] for item in x]))
fig = plt.figure(figsize = (15,10))
plt.axes()
ax1 = plt.subplot2grid((6,6), (0, 0), colspan=6, rowspan=4)
ax2 = plt.subplot2grid((6,6), (4, 0), colspan=6, rowspan=1, sharex = ax1)
#plt.gca().axes.get_yaxis().set_visible(False)
#l = aln[0][5]
tip = (right-left)/5000
ed = (right-left)/2000
grid_size = 1.0
ax1.set_xlim(left-2000,right+2000)
ax1.set_ylim(-5,num*grid_size)
points = [[left,0], [right,0], [right+tip,grid_size/4], [right,grid_size/2], [left,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)
ax1.add_patch(polygon)
dotted_line = plt.Line2D((left, left), (0, num*grid_size ),ls='-.')
ax1.add_line(dotted_line)
dotted_line2 = plt.Line2D((right, right), (0, num*grid_size ),ls='-.')
ax1.add_line(dotted_line2)
alns_all = []
for item in alns:
for aln in item:
alns_all.append([aln])
alns_all.sort(key = lambda x:min([item[3] for item in x]))
for i,aln_group in enumerate(alns_all):
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 = []
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]]
#if item[2] in bb:
# polygon = plt.Polygon(points,fc = 'r', ec = 'none', alpha = 0.8)
#else:
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")
ax1.add_patch(polygon)
if points_end != []:
polygon2 = plt.Polygon(points_end,fc = 'g', ec = 'none', alpha = 0.6)
ax1.add_patch(polygon2)
if points_start != []:
polygon2 = plt.Polygon(points_start,fc = 'g', ec = 'none', alpha = 0.6)
ax1.add_patch(polygon2)
ax2.plot(covx, covy)
plt.xlabel('position')
ax1.set_ylabel('pile-o-gram')
ax2.set_ylabel('coverage')
plt.savefig('mapping/map.' + str(contig) + '_' + str(left) +'_'+ str(right)+ '.svg')
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