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1 #!/usr/bin/env python
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2
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3 import os
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4 import sys
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5 import math
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6 import matplotlib as mpl
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7 mpl.use('PDF')
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8 import matplotlib.pyplot as plt
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9 from matplotlib.path import Path
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10 import matplotlib.patches as patches
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11
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12 ################################################################################
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13
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14 def build_chrom_len_dict(dbkey, galaxy_data_index_dir):
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15 chrom_len_root = os.path.join(galaxy_data_index_dir, 'shared/ucsc/chrom')
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16 chrom_len_file = '{0}.len'.format(dbkey)
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17 chrom_len_path = os.path.join(chrom_len_root, chrom_len_file)
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18
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19 chrom_len = {}
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20
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21 try:
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22 with open(chrom_len_path) as fh:
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23 for line in fh:
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24 line = line.rstrip('\r\n')
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25 elems = line.split()
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26 if len(elems) == 2:
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27 chrom = elems[0]
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28 length = int(elems[1])
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29 chrom_len[chrom] = length
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30 except:
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31 pass
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32
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33 return chrom_len
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34
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35 def parse_input_file(input_file):
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36 chroms = []
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37 individuals = []
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38 data = {}
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39 chrom_len = {}
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40
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41 with open(input_file) as fh:
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42 for line in fh:
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43 line = line.strip()
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44 if line:
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45 elems = line.split()
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46 chrom = elems[0]
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47 p1, p2, state = map(int, elems[1:4])
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48 id = elems[4]
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49
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50 if chrom not in chroms:
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51 chroms.append(chrom)
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52
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53 if id not in individuals:
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54 individuals.append(id)
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55
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56 data.setdefault(chrom, {})
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57 data[chrom].setdefault(id, [])
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58 data[chrom][id].append((p1, p2, state))
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59
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60 if p2 > chrom_len.setdefault(chrom, 0):
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61 chrom_len[chrom] = p2
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62
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63 return chroms, individuals, data, chrom_len
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64
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65 def check_chroms(chroms, chrom_len, dbkey):
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66 error = 0
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67 for chrom in chroms:
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68 if chrom not in chrom_len:
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69 print >> sys.stderr, "Can't find length for {0} chromosome {1}".format(dbkey, chrom)
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70 error = 1
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71 if error:
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72 sys.exit(1)
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73
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74 def check_data(data, chrom_len, dbkey):
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75 error = 0
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76 for chrom in data:
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77 chrom_beg = 0
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78 chrom_end = chrom_len[chrom]
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79 for individual in data[chrom]:
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80 for p1, p2, state in data[chrom][individual]:
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81 if p1 >= p2:
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82 print >> sys.stderr, "Bad data line: begin >= end: {0} {1} {2} {3}".format(chrom, p1, p2, state, individual)
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83 error = 1
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84 if p1 < chrom_beg or p2 > chrom_end:
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85 print >> sys.stderr, "Bad data line: outside {0} boundaries[{1} - {2}]: {3} {4} {5} {6}".format(dbkey, chrom_beg, chrom_end, chrom, p1, p2, state, individual)
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86 error = 1
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87 if error:
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88 sys.exit(1)
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89
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90 def make_rectangle(p1, p2, color, bottom=0.0, top=1.0):
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91 verts = [
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92 (p1, bottom), # left, bottom
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93 (p1, top), # left, top
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94 (p2, top), # right, top
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95 (p2, bottom), # right, bottom
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96 (0.0, 0.0) # ignored
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97 ]
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98
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99 codes = [
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100 Path.MOVETO,
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101 Path.LINETO,
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102 Path.LINETO,
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103 Path.LINETO,
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104 Path.CLOSEPOLY
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105 ]
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106
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107 path = Path(verts, codes)
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108 return patches.PathPatch(path, facecolor=color, lw=0)
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109
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110 def make_split_rectangle(p1, p2, top_color, bottom_color):
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111 patch1 = make_rectangle(p1, p2, bottom_color, top=0.5)
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112 patch2 = make_rectangle(p1, p2, top_color, bottom=0.5)
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113 return [patch1, patch2]
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114
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115 def make_state_rectangle(p1, p2, state, chrom, individual):
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116 if state == 0:
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117 return [ make_rectangle(p1, p2, 'r') ]
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118 elif state == 1:
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119 return make_split_rectangle(p1, p2, 'r', 'g')
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120 elif state == 2:
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121 return [ make_rectangle(p1, p2, 'g') ]
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122 elif state == 3:
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123 return [ make_rectangle(p1, p2, '#c7c7c7') ]
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124 else:
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125 print >> sys.stderr, "Unknown state: {0}: {1} {2} {3} {4}".format(state, chrom, p1, p2, state, individual)
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126 sys.exit(1)
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127
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128 def nicenum(num, round=False):
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129 if num == 0:
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130 return 0.0
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131
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132 exp = int(math.floor(math.log10(num)))
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133 f = num / math.pow(10, exp)
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134
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135 if round:
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136 if f < 1.5:
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137 nf = 1.0
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138 elif f < 3.0:
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139 nf = 2.0
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140 elif f < 7.0:
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141 nf = 5.0
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142 else:
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143 nf = 10.0
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144 else:
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145 if f <= 1.0:
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146 nf = 1.0
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147 elif f <= 2.0:
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148 nf = 2.0
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149 elif f <= 5.0:
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150 nf = 5.0
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151 else:
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152 nf = 10.0
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153
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154 return nf * pow(10, exp)
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155
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156 def tick_foo(beg, end, loose=False):
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157 ntick = 10
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158
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159 range = nicenum(end - beg, round=False)
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160 d = nicenum(range/(ntick - 1), round=True)
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161 digits = int(math.floor(math.log10(d)))
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162
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163 if loose:
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164 graph_min = math.floor(beg/d) * d
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165 graph_max = math.ceil(end/d) * d
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166 else:
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167 graph_min = beg
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168 graph_max = end
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169
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170 nfrac = max([-1 * digits, 0])
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171 vals = []
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172
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173 stop = graph_max
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174 if loose:
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175 stop = graph_max + (0.5 * d)
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176
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177 x = graph_min
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178 while x <= stop:
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179 vals.append(int(x))
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180 x += d
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181
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182 vals = vals[1:]
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183
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184 # if not loose:
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185 # if vals[-1] < graph_max:
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186 # vals.append(int(graph_max))
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187
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188 labels = []
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189 for val in vals:
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190 labels.append('{0}'.format(int(val/math.pow(10, digits))))
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191
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192 # labels.append('{0:.1f}'.format(vals[-1]/math.pow(10, digits)))
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193
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194 return vals, labels
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195
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196 ################################################################################
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197
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198 def make_dpmix_plot(input_dbkey, input_file, output_file, galaxy_data_index_dir):
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199 fs_chrom_len = build_chrom_len_dict(input_dbkey, galaxy_data_index_dir)
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200 chroms, individuals, data, chrom_len = parse_input_file(input_file)
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201
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202 for chrom in chrom_len.keys():
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203 if chrom in fs_chrom_len:
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204 chrom_len[chrom] = fs_chrom_len[chrom]
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205
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206 #check_chroms(chroms, chrom_len, input_dbkey)
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207 check_data(data, chrom_len, input_dbkey)
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208
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209 ## units below are inches
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210 top_space = 0.10
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211 chrom_space = 0.25
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212 chrom_height = 0.25
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213 ind_space = 0.10
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214 ind_height = 0.25
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215
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216 total_height = 0.0
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217 at_top = True
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218 for chrom in chroms:
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219 if at_top:
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220 total_height += (top_space + chrom_height)
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221 at_top = False
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222 else:
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223 total_height += (top_space + chrom_space + chrom_height)
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224
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225 individual_count = 0
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226 for individual in individuals:
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227 if individual in data[chrom]:
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228 individual_count += 1
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229 total_height += individual_count * (ind_space + ind_height)
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230
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231 width = 7.5
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232 height = math.ceil(total_height)
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233
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234 bottom = 1.0
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235
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236 fig = plt.figure(figsize=(width, height))
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237
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238 at_top = True
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239 for_webb = False
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240
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241 for chrom in chroms:
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242 length = chrom_len[chrom]
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243 vals, labels = tick_foo(0, length)
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244
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245 if at_top:
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246 bottom -= (top_space + chrom_height)/height
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247 at_top = False
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248 else:
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249 bottom -= (top_space + chrom_space + chrom_height)/height
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250
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251 if not for_webb:
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252 ax = fig.add_axes([0.0, bottom, 1.0, chrom_height/height])
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253 plt.axis('off')
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254 plt.text(0.5, 0.5, chrom, fontsize=14, ha='center')
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255
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256 individual_count = 0
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257 for individual in individuals:
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258 if individual in data[chrom]:
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259 individual_count += 1
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260
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261 i = 0
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262 for individual in individuals:
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263 if individual in data[chrom]:
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264 i += 1
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265
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266 bottom -= (ind_space + ind_height)/height
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267 if not for_webb:
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268 # [left, bottom, width, height]
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269 ax1 = fig.add_axes([0.0, bottom, 0.09, ind_height/height])
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270 plt.axis('off')
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271 plt.text(1.0, 0.5, individual, fontsize=10, ha='right', va='center')
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272 # [left, bottom, width, height]
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273 ax2 = fig.add_axes([0.10, bottom, 0.88, ind_height/height], frame_on=False)
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274 ax2.set_xlim(0, length)
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275 ax2.set_ylim(0, 1)
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276 if i != individual_count:
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277 plt.axis('off')
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278 else:
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279 if not for_webb:
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280 ax2.tick_params(top=False, left=False, right=False, labelleft=False)
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281 ax2.set_xticks(vals)
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282 ax2.set_xticklabels(labels)
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283 else:
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284 plt.axis('off')
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285 for p1, p2, state in sorted(data[chrom][individual]):
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286 for patch in make_state_rectangle(p1, p2, state, chrom, individual):
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287 ax2.add_patch(patch)
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288
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289 plt.savefig(output_file)
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290
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291 ################################################################################
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292
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293 if __name__ == '__main__':
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294 input_dbkey, input_file, output_file, galaxy_data_index_dir = sys.argv[1:5]
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295 make_dpmix_plot(input_dbkey, input_file, output_file, galaxy_data_index_dir)
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296 sys.exit(0)
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297
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