1 | #!/usr/bin/env python |
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2 | |
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3 | from galaxy import eggs |
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4 | import sys, tempfile, os |
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5 | |
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6 | assert sys.version_info[:2] >= (2.4) |
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7 | |
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8 | def stop_err(msg): |
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9 | sys.stderr.write(msg) |
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10 | sys.exit() |
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11 | |
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12 | def main(): |
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13 | |
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14 | out_fname = sys.argv[1] |
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15 | in_fname = sys.argv[2] |
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16 | chr_col = int(sys.argv[3])-1 |
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17 | coord_col = int(sys.argv[4])-1 |
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18 | track_type = sys.argv[5] |
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19 | if track_type == 'coverage' or track_type == 'both': |
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20 | coverage_col = int(sys.argv[6])-1 |
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21 | cname = sys.argv[7] |
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22 | cdescription = sys.argv[8] |
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23 | ccolor = sys.argv[9].replace('-',',') |
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24 | cvisibility = sys.argv[10] |
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25 | if track_type == 'snp' or track_type == 'both': |
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26 | if track_type == 'both': |
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27 | j = 5 |
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28 | else: |
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29 | j = 0 |
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30 | #sname = sys.argv[7+j] |
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31 | sdescription = sys.argv[6+j] |
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32 | svisibility = sys.argv[7+j] |
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33 | #ref_col = int(sys.argv[10+j])-1 |
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34 | read_col = int(sys.argv[8+j])-1 |
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35 | |
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36 | |
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37 | # Sort the input file based on chromosome (alphabetically) and start co-ordinates (numerically) |
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38 | sorted_infile = tempfile.NamedTemporaryFile() |
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39 | try: |
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40 | os.system("sort -k %d,%d -k %dn -o %s %s" %(chr_col+1,chr_col+1,coord_col+1,sorted_infile.name,in_fname)) |
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41 | except Exception, exc: |
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42 | stop_err( 'Initialization error -> %s' %str(exc) ) |
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43 | |
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44 | #generate chr list |
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45 | sorted_infile.seek(0) |
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46 | chr_vals = [] |
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47 | for line in file( sorted_infile.name ): |
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48 | line = line.strip() |
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49 | if not(line): |
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50 | continue |
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51 | try: |
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52 | fields = line.split('\t') |
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53 | chr = fields[chr_col] |
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54 | if chr not in chr_vals: |
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55 | chr_vals.append(chr) |
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56 | except: |
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57 | pass |
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58 | if not(chr_vals): |
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59 | stop_err("Skipped all lines as invalid.") |
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60 | |
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61 | if track_type == 'coverage' or track_type == 'both': |
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62 | if track_type == 'coverage': |
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63 | fout = open( out_fname, "w" ) |
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64 | else: |
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65 | fout = tempfile.NamedTemporaryFile() |
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66 | fout.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ |
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67 | % ( cname, cdescription, ccolor, cvisibility )) |
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68 | if track_type == 'snp' or track_type == 'both': |
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69 | fout_a = tempfile.NamedTemporaryFile() |
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70 | fout_t = tempfile.NamedTemporaryFile() |
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71 | fout_g = tempfile.NamedTemporaryFile() |
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72 | fout_c = tempfile.NamedTemporaryFile() |
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73 | fout_ref = tempfile.NamedTemporaryFile() |
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74 | |
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75 | fout_a.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ |
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76 | % ( "Track A", sdescription, '255,0,0', svisibility )) |
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77 | fout_t.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ |
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78 | % ( "Track T", sdescription, '0,255,0', svisibility )) |
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79 | fout_g.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ |
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80 | % ( "Track G", sdescription, '0,0,255', svisibility )) |
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81 | fout_c.write('''track type=wiggle_0 name="%s" description="%s" color=%s visibility=%s\n''' \ |
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82 | % ( "Track C", sdescription, '255,0,255', svisibility )) |
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83 | |
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84 | |
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85 | sorted_infile.seek(0) |
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86 | for line in file( sorted_infile.name ): |
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87 | line = line.strip() |
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88 | if not(line): |
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89 | continue |
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90 | try: |
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91 | fields = line.split('\t') |
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92 | chr = fields[chr_col] |
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93 | start = int(fields[coord_col]) |
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94 | assert start > 0 |
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95 | except: |
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96 | continue |
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97 | try: |
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98 | ind = chr_vals.index(chr) #encountered chr for the 1st time |
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99 | del chr_vals[ind] |
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100 | prev_start = '' |
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101 | header = "variableStep chrom=%s\n" %(chr) |
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102 | if track_type == 'coverage' or track_type == 'both': |
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103 | coverage = int(fields[coverage_col]) |
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104 | line1 = "%s\t%s\n" %(start,coverage) |
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105 | fout.write("%s%s" %(header,line1)) |
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106 | if track_type == 'snp' or track_type == 'both': |
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107 | a = t = g = c = 0 |
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108 | fout_a.write("%s" %(header)) |
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109 | fout_t.write("%s" %(header)) |
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110 | fout_g.write("%s" %(header)) |
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111 | fout_c.write("%s" %(header)) |
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112 | try: |
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113 | #ref_nt = fields[ref_col].capitalize() |
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114 | read_nt = fields[read_col].capitalize() |
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115 | try: |
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116 | nt_ind = ['A','T','G','C'].index(read_nt) |
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117 | if nt_ind == 0: |
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118 | a+=1 |
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119 | elif nt_ind == 1: |
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120 | t+=1 |
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121 | elif nt_ind == 2: |
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122 | g+=1 |
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123 | else: |
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124 | c+=1 |
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125 | except ValueError: |
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126 | pass |
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127 | except: |
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128 | pass |
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129 | prev_start = start |
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130 | except ValueError: |
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131 | if start != prev_start: |
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132 | if track_type == 'coverage' or track_type == 'both': |
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133 | coverage = int(fields[coverage_col]) |
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134 | fout.write("%s\t%s\n" %(start,coverage)) |
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135 | if track_type == 'snp' or track_type == 'both': |
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136 | if a: |
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137 | fout_a.write("%s\t%s\n" %(prev_start,a)) |
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138 | if t: |
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139 | fout_t.write("%s\t%s\n" %(prev_start,t)) |
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140 | if g: |
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141 | fout_g.write("%s\t%s\n" %(prev_start,g)) |
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142 | if c: |
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143 | fout_c.write("%s\t%s\n" %(prev_start,c)) |
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144 | a = t = g = c = 0 |
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145 | try: |
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146 | #ref_nt = fields[ref_col].capitalize() |
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147 | read_nt = fields[read_col].capitalize() |
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148 | try: |
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149 | nt_ind = ['A','T','G','C'].index(read_nt) |
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150 | if nt_ind == 0: |
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151 | a+=1 |
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152 | elif nt_ind == 1: |
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153 | t+=1 |
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154 | elif nt_ind == 2: |
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155 | g+=1 |
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156 | else: |
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157 | c+=1 |
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158 | except ValueError: |
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159 | pass |
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160 | except: |
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161 | pass |
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162 | prev_start = start |
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163 | else: |
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164 | if track_type == 'snp' or track_type == 'both': |
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165 | try: |
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166 | #ref_nt = fields[ref_col].capitalize() |
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167 | read_nt = fields[read_col].capitalize() |
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168 | try: |
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169 | nt_ind = ['A','T','G','C'].index(read_nt) |
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170 | if nt_ind == 0: |
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171 | a+=1 |
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172 | elif nt_ind == 1: |
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173 | t+=1 |
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174 | elif nt_ind == 2: |
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175 | g+=1 |
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176 | else: |
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177 | c+=1 |
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178 | except ValueError: |
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179 | pass |
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180 | except: |
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181 | pass |
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182 | |
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183 | if track_type == 'snp' or track_type == 'both': |
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184 | if a: |
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185 | fout_a.write("%s\t%s\n" %(prev_start,a)) |
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186 | if t: |
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187 | fout_t.write("%s\t%s\n" %(prev_start,t)) |
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188 | if g: |
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189 | fout_g.write("%s\t%s\n" %(prev_start,g)) |
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190 | if c: |
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191 | fout_c.write("%s\t%s\n" %(prev_start,c)) |
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192 | |
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193 | fout_a.seek(0) |
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194 | fout_g.seek(0) |
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195 | fout_t.seek(0) |
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196 | fout_c.seek(0) |
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197 | |
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198 | if track_type == 'snp': |
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199 | os.system("cat %s %s %s %s >> %s" %(fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname)) |
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200 | elif track_type == 'both': |
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201 | fout.seek(0) |
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202 | os.system("cat %s %s %s %s %s | cat > %s" %(fout.name,fout_a.name,fout_t.name,fout_g.name,fout_c.name,out_fname)) |
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203 | if __name__ == "__main__": |
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204 | main() |
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