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1 """
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2 @summary: Save partial z file
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3 @version 7
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4
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5 """
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6 # MAPPER --> save z file
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7
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8 # Input: qtlcart.inp
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9 # qtlcart.map
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10 # parameters.txt
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11
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12 # Output: z_partial.txt
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13
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14 import optparse, sys
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15 import tempfile
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16 import re
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17
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18 def stop_err( msg ):
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19 sys.stderr.write( "%s\n" % msg )
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20 sys.exit()
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21
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22 def __main__():
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23 parser = optparse.OptionParser()
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24 parser.add_option("-i", "--input1", default=None, dest="input1",
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25 help="qtlcart.inp file")
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26 parser.add_option("-j", "--input2", default=None, dest="input2",
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27 help="qtlcart.map file")
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28 parser.add_option("-k", "--input3", default=None, dest="input3",
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29 help="parameters.txt file")
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30
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31 parser.add_option("-p", "--output1", default=None, dest="output1",
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32 help="qtlcart_partial.z file")
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33 (options, args) = parser.parse_args()
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34
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35 try:
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36 open(options.input1, "r").close()
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37 except TypeError, e:
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38 stop_err("You need to supply the qtlcart.inp file:\n" + str(e))
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39 except IOError, e:
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40 stop_err("Can not open the qtlcart.inp file:\n" + str(e))
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41
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42 try:
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43 open(options.input2, "r").close()
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44 except TypeError, e:
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45 stop_err("You need to supply the qtlcart.map file:\n" + str(e))
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46 except IOError, e:
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47 stop_err("Can not open the qtlcart.map file:\n" + str(e))
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48
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49 try:
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50 open(options.input3, "r").close()
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51 except TypeError, e:
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52 stop_err("You need to supply the parameters.txt file:\n" + str(e))
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53 except IOError, e:
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54 stop_err("Can not open the parameters.txt file:\n" + str(e))
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55
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56 ######################################################################
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57 # submit.py
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58 ######################################################################
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59
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60 import subprocess
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61 import os
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62
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63 # Create temp direcotry
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64 tempdir = tempfile.mkdtemp()
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65 #print tempdir
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66
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67 s = "cp %s %s/parameters.txt" %(options.input3, tempdir)
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68 subprocess.call(s, shell=True)
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69 paramters_file = open(tempdir+"/parameters.txt", "r")
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70 parvalues = []
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71 for line in paramters_file:
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72 l = line.strip().split("\t")
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73 if l[0] == "SRmodel":
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74 SRmodel = l[1]
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75 if l[0] == "Zmodel":
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76 Zmodel = l[1]
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77 if l[0] == "threshold":
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78 threshold = l[1]
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79 if l[0] == "walking_speed":
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80 walking_speed = l[1]
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81 if l[0] == "window_size":
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82 window_size = l[1]
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83 if l[0] == "minimum_cM_between_QTL":
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84 minimum_cM_between_QTL = l[1]
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85 paramters_file.close()
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86
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87 # copy INPUT file to the temp directory
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88 s = "cp %s %s/qtlcart.inp" %(options.input1, tempdir)
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89 subprocess.call(s, shell=True)
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90 s = "cp %s %s/qtlcart.map" %(options.input2, tempdir)
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91 subprocess.call(s, shell=True)
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92
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93 f=open(tempdir+"/qtlcart.inp", "r")
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94 ln=f.readlines()
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95 f.close()
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96 count = 0
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97
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98 if ln[0] == "NA":
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99 f1=open(tempdir+"/QTLs_total_parsed_LOD.txt", "w")
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100 f1.write("")
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101 f1.close()
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102 os.system("mv %s/QTLs_total_parsed_LOD.txt %s" %(tempdir,options.output1))
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103 #os.system("mv %s/qtlcart.rc %s" %(tempdir,options.output2))
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104 else:
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105 count += 1
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106 if count == 1:
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107 instruction = "/cluster1/bin/Rcross -i %s/qtlcart.inp -o %s/qtlcart.cro -A -V" %(tempdir, tempdir)
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108 os.system(instruction)
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109
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110 instruction = "/cluster1/bin/SRmapqtl -i %s/qtlcart.cro -e %s/SRqtlcart.log -o %s/qtlcart.sr -m %s/qtlcart.map -M %s -t 9999999999 -A -V" %(tempdir, tempdir, tempdir, tempdir, str(SRmodel))
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111 os.system(instruction)
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112
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113 instruction = "/cluster1/bin/Zmapqtl -i %s/qtlcart.cro -o %s/qtlcart.z -m %s/qtlcart.map -S %s/qtlcart.sr -M %s -d %s -w %s -t 9999999999 -A -V" %(tempdir, tempdir, tempdir, tempdir, str(Zmodel), str(walking_speed), str(window_size))
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114 os.system(instruction)
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115
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116 #####################
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117 # Save partial z file
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118 #####################
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119
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120 zfile=open(tempdir+"/qtlcart_partial.z", "w")
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121 f=open(tempdir+"/qtlcart.z", "r")
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122 done = "no"
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123 for l in f:
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124 if (done != "yes") and (not l.startswith("-e")):
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125 zfile.write(l.strip()+"\n")
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126 else:
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127 done = "yes"
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128 f.close()
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129 zfile.write("-e\n")
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130 zfile.close()
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131
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132 os.system("mv %s/qtlcart_partial.z %s" %(tempdir,options.output1))
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133
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134 if __name__=="__main__":
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135 __main__()
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136
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137
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