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1 #!/usr/bin/python
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2 # -*- coding: utf-8 -*-
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3
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4 import sys
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5 import re
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6 import os
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7 import tempfile
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8 import shutil
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9 import subprocess
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10 import glob
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11 import argparse
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12 from os.path import basename
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13 import zipfile
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14 import tarfile
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15 import gzip
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16 from galaxy.datatypes.checkers import *
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17 from stacks import *
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18
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19
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20 def __main__():
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21
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22 # arguments recuperation
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23
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24 parser = argparse.ArgumentParser()
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25 parser.add_argument('-P')
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26 parser.add_argument('-M')
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27 parser.add_argument('-b')
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28 parser.add_argument('--vcf', action='store_true')
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29 parser.add_argument('--genepop', action='store_true')
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30 parser.add_argument('--structure', action='store_true')
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31 parser.add_argument('-e')
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32 parser.add_argument('--genomic', action='store_true')
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33 parser.add_argument('--fasta', action='store_true')
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34 parser.add_argument('--phase', action='store_true')
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35 parser.add_argument('--beagle', action='store_true')
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36 parser.add_argument('--plink', action='store_true')
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37 parser.add_argument('--phylip', action='store_true')
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38 parser.add_argument('--phylip_var', action='store_true')
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39 parser.add_argument('--write_single_snp', action='store_true')
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40 parser.add_argument('-k', action='store_true')
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41
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42 # advanced options
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43 parser.add_argument('--advanced_options_activate')
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44 parser.add_argument('-B')
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45 parser.add_argument('-W')
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46 parser.add_argument('-r')
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47 parser.add_argument('-p')
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48 parser.add_argument('-m')
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49 parser.add_argument('-a')
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50 parser.add_argument('-f')
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51 parser.add_argument('--p_value_cutoff')
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52 parser.add_argument('--window_size')
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53 parser.add_argument('--bootstrap')
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54 parser.add_argument('--bootstrap_reps')
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55
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56 # multifile management
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57 parser.add_argument('--logfile')
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58
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59 # outputs
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60 parser.add_argument('--ss')
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61 parser.add_argument('--s')
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62
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63 # optional outputs
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64 parser.add_argument('--ov')
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65 parser.add_argument('--op')
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66 parser.add_argument('--ol')
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67 parser.add_argument('--of')
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68 parser.add_argument('--os')
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69 parser.add_argument('--oe')
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70 parser.add_argument('--om')
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71 parser.add_argument('--og')
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72
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73 parser.add_argument('--unphased_output')
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74 parser.add_argument('--markers_output')
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75 parser.add_argument('--phase_output')
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76 parser.add_argument('--fst_output')
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77
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78 options = parser.parse_args()
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79
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80 # create the working dir
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81 os.mkdir('job_outputs')
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82 os.mkdir('galaxy_outputs')
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83
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84 os.chdir('job_outputs')
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85
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86 # STACKS_archive
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87 # check if zipped files are into the tab
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88 extract_compress_files(options.P, os.getcwd())
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89
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90 # create the populations command input line
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91 cmd_line=['populations']
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92 cmd_line.extend(['-b', options.b, '-P', os.getcwd(), '-M', options.M])
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93
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94 if options.e:
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95 cmd_line.extend(['-e', options.e, options.genomic])
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96
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97 # output options
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98 if options.vcf:
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99 cmd_line.append('--vcf')
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100 if options.genepop:
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101 cmd_line.append('--genepop')
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102 if options.structure:
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103 cmd_line.append('--structure')
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104 if options.fasta:
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105 cmd_line.append('--fasta')
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106 if options.phase:
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107 cmd_line.append('--phase')
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108 if options.beagle:
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109 cmd_line.append('--beagle')
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110 if options.plink:
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111 cmd_line.append('--plink')
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112 if options.phylip:
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113 cmd_line.append('--phylip')
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114 if options.phylip_var and options.phylip:
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115 cmd_line.append('--phylip_var')
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116 if options.write_single_snp and (options.genepop or options.structure):
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117 cmd_line.append('--write_single_snp')
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118
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119 if options.k:
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120 cmd_line.extend(['-k', '--window_size', options.window_size])
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121
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122 if options.advanced_options_activate == 'true':
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123 if options.B:
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124 cmd_line.extend(['-B', options.B])
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125 if options.W:
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126 cmd_line.extend(['-W', options.W])
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127
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128 cmd_line.extend(['-r', options.r])
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129 cmd_line.extend(['-p', options.p])
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130 cmd_line.extend(['-m', options.m])
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131 cmd_line.extend(['-a', options.a])
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132
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133 if options.f:
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134 cmd_line.extend(['-f', options.f, '--p_value_cutoff', options.p_value_cutoff])
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135 if options.bootstrap:
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136 cmd_line.extend(['--bootstrap', options.bootstrap, '--bootstrap_reps', options.bootstrap_reps])
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137
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138 print "[CMD]:"+' '.join(cmd_line)
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139 subprocess.call(cmd_line)
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140
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141 # postprocesses
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142 try:
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143 shutil.copy('batch_1.populations.log', options.logfile)
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144 except:
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145 sys.stderr.write('Error in population execution; Please read the additional output (stdout)\n')
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146 sys.exit(1)
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147
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148 try:
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149 shutil.move(glob.glob('*.sumstats_summary.tsv')[0], options.ss)
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150 except:
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151 print "No sumstats summary file"
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152
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153 try:
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154 shutil.move(glob.glob('*.sumstats.tsv')[0], options.s)
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155 except:
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156 print "No sumstats file"
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157
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158 # move additionnal output files
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159 if options.vcf:
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160 try:
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161 shutil.move(glob.glob('*.vcf')[0], options.ov)
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162 except:
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163 print "No VCF files"
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164
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165 if options.phylip:
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166 try:
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167 shutil.move(glob.glob('*.phylip')[0], options.op)
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168 shutil.move(glob.glob('*.phylip.log')[0], options.ol)
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169 except:
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170 print "No phylip file"
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171
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172 if options.fasta:
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173 try:
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174 shutil.move(glob.glob('*.fa')[0], options.of)
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175 except:
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176 print "No fasta files"
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177
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178 if options.structure:
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179 try:
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180 shutil.move(glob.glob('*.structure.tsv')[0], options.os)
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181 except:
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182 print "No structure file"
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183
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184 if options.plink :
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185 try:
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186 shutil.move(glob.glob('*.ped')[0], options.oe)
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187 shutil.move(glob.glob('*.map')[0], options.om)
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188 except:
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189 print "No ped and map file"
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190
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191 if options.genepop :
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192 try:
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193 shutil.move(glob.glob('*.genepop')[0], options.og)
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194 except:
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195 print "No genepop file"
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196
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197 # copy all files inside tmp_dir into workdir or into an archive....
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198 list_files = glob.glob('*')
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199
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200 markerszip = zipfile.ZipFile('markers.zip.temp', 'w',
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201 allowZip64=True)
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202 phasezip = zipfile.ZipFile('phase.zip.temp', 'w', allowZip64=True)
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203 unphasedzip = zipfile.ZipFile('unphased.zip.temp', 'w',
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204 allowZip64=True)
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205 fstzip = zipfile.ZipFile('fst.zip.temp', 'w', allowZip64=True)
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206
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207 for i in list_files:
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208 # for each type of files
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209 if re.search("\.markers$", i):
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210 markerszip.write(i)
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211 elif re.search("phase\.inp$", i):
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212 phasezip.write(i)
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213 elif re.search("unphased\.bgl$", i):
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214 unphasedzip.write(i)
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215 elif re.search('fst', i):
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216 fstzip.write(i)
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217 else:
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218 # else return original files
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219 if re.search('^batch', os.path.basename(i)) \
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220 and not re.search("\.tsv$", os.path.basename(i)) \
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221 or re.search(".*_[0-9]*\.tsv$", os.path.basename(i)):
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222 shutil.move(i, '../galaxy_outputs')
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223
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224 # close zip files
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225 markerszip.close()
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226 phasezip.close()
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227 unphasedzip.close()
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228 fstzip.close()
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229
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230 # return archives
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231 shutil.move('fst.zip.temp', options.fst_output)
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232 if options.beagle:
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233 shutil.move('markers.zip.temp', options.markers_output)
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234 shutil.move('unphased.zip.temp', options.unphased_output)
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235 if options.phase:
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236 shutil.move('phase.zip.temp', options.phase_output)
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237
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238
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239 if __name__ == '__main__':
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240 __main__()
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241
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242
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243
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