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9
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1 #!/usr/bin/env python
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2 import argparse, os, shutil, sys, tempfile, subprocess
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3
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4
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5 class sampleContainer:
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6 def __init__(self):
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7 self.samples = []
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8 self.pairs = []
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9 self.pair_index = {}
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10 self.treatments = {}
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11 self.treatment_types = {}
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12 self.names = {}
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13
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14 def add_sample(self,sample):
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15 if(sample in self.samples):
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16 sys.stderr.write("Error:\n* Sample has been added multiple times: "+sample+"\n")
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17 sys.exit(1)
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18 else:
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19 self.samples.append(sample)
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20 print " - Added: "+sample
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21
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22 def add_pair(self,pair):
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23 print " - Adding pair:"
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24 for sample in pair:
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25 self.add_sample(sample)
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26 self.pairs.append(pair)
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27 pair_id = len(self.pairs)
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28
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29 for sample in pair:
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30 self.pair_index[sample] = pair_id
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31
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32 def add_treatment_argument(self,treatment_argument,name=None):
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33 print " - Parsing treatment"
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34
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35 treatment = {"factor_index":{},"sample_index":{}}
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36 only_integers = True
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37
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38 i = 1
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39 for item in treatment_argument:
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40 if(i % 2):
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41 factor = item
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42 if(treatment['factor_index'].has_key(factor)):
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43 sys.stderr.write("Error:\n* Factor has been added multiple times to treatment: "+factor+"\n")
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44 else:
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45 print " - Adding factor: "+factor
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46 treatment["factor_index"][factor] = []
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47 if(not factor.isdigit()):
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48 only_integers = False
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49 else:
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50 for sample in item.split(","):
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51 treatment["factor_index"][factor].append(sample)
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52 if(treatment["sample_index"].has_key(sample)):
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53 sys.stderr.write("Error:\n* Factor has been added to treatment before: "+sample+"/"+factor+", factors must be mutually exclusive!\n")
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54 else:
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55 treatment["sample_index"][sample] = factor
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56 i += 1
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57
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58 treatment_factors = sorted(treatment["factor_index"].keys())
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59
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60 if(name == None):
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61 treatment["name"] = "_vs_".join(treatment_factors)
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62 else:
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63 treatment["name"] = str(name)
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64
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65 if(len(treatment["sample_index"]) != len(self.samples)):
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66 sys.stderr.write("Error:\n* The number of samples for treatment '"+treatment["name"]+"' ("+str(len(treatment["sample_index"]))+") is different from the total number of samples ("+str(len(self.samples))+").\n")
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67
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68 if(only_integers):
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69 treatment_type = "integer"
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70 else:
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71 treatment_type = "string"
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72
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73 if(self.treatments.has_key(treatment["name"])):
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74 sys.stderr.write("Error:\n* Treatment was already added: '"+treatment["name"]+"\n")
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75 else:
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76 self.treatments[treatment["name"]] = treatment
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77 self.treatment_types[treatment["name"]] = treatment_type
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78 print " - Treatment of type: "+treatment_type+" is valid: "+treatment["name"]
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79
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80 def add_names_argument(self,names_argument):
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81 for sample in names_argument:
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82 self.add_name(sample)
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83
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84 def add_name(self,argument):
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85 argument = argument.split(":",1)
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86 self.names[argument[0]] = argument[1]
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87
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88 def add_unpaired_samples_argument(self,argument):
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89 print " - Adding unpaired samples"
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90 for sample in argument:
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91 self.add_sample(sample)
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92
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93 def add_paired_samples_argument(self,argument):
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94 print " - Adding paired samples"
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95 pair = []
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96 for potential_sample in argument:
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97 if(potential_sample == ":"):
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98 self.add_pair(pair)
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99 pair = []
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100 else:
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101 pair.append(potential_sample)
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102
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103 def add_treatments_argument(self,argument):
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104 print " - Adding treatments"
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105 treatment_argument = []
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106 for potential_treatment in argument:
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107 if(potential_treatment == ":"):
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108 self.add_treatment_argument(treatment_argument)
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109 treatment_argument = []
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110 else:
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111 treatment_argument.append(potential_treatment)
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112
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113 def add_pairings(self):
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114 samples = sorted(self.samples)
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115 treatment_arguments = []
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116
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117 if len(self.pairs) > 0:
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118 for pair_id in range(len(self.pairs)):
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119 # add to treatments
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120 treatment_arguments.append(str(pair_id+1))
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121 treatment_arguments.append(",".join(self.pairs[pair_id]))
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122
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123 # remove from samples
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124 for sample in self.pairs[pair_id]:
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125 samples.remove(sample)
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126
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127 # Add remaining samples as separate factors
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128 i = len(self.pairs)+1
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129 for sample in samples:
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130 treatment_arguments.append(str(i))
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131 treatment_arguments.append(sample)
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132 i += 1
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133
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134 treatment_arguments.append(":")
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135
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136 self.add_treatments_argument(treatment_arguments)
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137
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138 def export(self,output):
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139 # Open file stream
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140 if(args.output == "-"):
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141 fh = sys.stdout
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142 else:
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143 fh = open(args.output,"w")
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144
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145 # Write header:
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146 fh.write("filename\tname\t"+"\t".join(self.treatments.keys())+"\n")
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147
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148 #fh.write("#\ttype")
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149 #for treatment in self.treatments.keys():
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150 # fh.write("\t"+self.treatment_types[treatment])
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151 #fh.write("\n")
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152
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153 # Write body:
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154 for sample in self.samples:
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155 fh.write(sample+"\t"+self.names[sample])
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156 for treatment in self.treatments.keys():
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157 fh.write("\t"+self.treatments[treatment]["sample_index"][sample])
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158 fh.write("\n")
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159
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160 fh.close()
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161
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162 if __name__=="__main__":
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163 parser = argparse.ArgumentParser(description="Create an edgeR design matrix with read-count datasets.")
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164 parser.add_argument("-o","--output", help="Output file, '-' for stdout.",required=True)
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165 parser.add_argument("-u","--unpaired-samples", nargs="*", help='Unpaired sample files.')
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166 parser.add_argument("-p","--paired-samples", nargs="*", help='Paired sample files: pat_x_sample_1.txt, .')
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167 parser.add_argument("-t","--treatments", nargs="+", help='Treatment conditions',required=True)
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168 parser.add_argument("-n","--sample-names", nargs="+", help='Paired sample files: pat_x_sample_1.txt:NAME .')
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169
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170 args = parser.parse_args()
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171
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172 s = sampleContainer()
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173 s.add_unpaired_samples_argument(args.unpaired_samples)
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174 s.add_paired_samples_argument(args.paired_samples)
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175 s.add_treatments_argument(args.treatments)
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176 s.add_names_argument(args.sample_names)
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177 s.add_pairings()
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178 s.export(args.output)
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