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1 function [CFG]=process_command_line_args(CFG,ARGS)
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2 % [CFG]=process_command_line_args(CFG,ARGS)
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3
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4 %This function adds the command line arguments to the CFG config variable
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5
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6 %Parse the ARGS
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7
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8 %Check wether octave or matlab is used
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9 if size(ver('Octave'),1)
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10 INTERPR = 1;
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11 else
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12 INTERPR = 0;
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13 end
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14
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15 %turn of warning
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16 if INTERPR
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17 warning('off', 'Octave:precedence-change');
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18 warning('off', 'Octave:function-name-clash');
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19 warning('off', '');
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20 warning('off', 'Octave:num-to-str');
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21 warning('off', 'Octave:function-name-clash');
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22 warning('off', 'Octave:divide-by-zero');
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23 warning('off', 'Octave:future-time-stamp');
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24 warning('off', 'solve_qp:constraints');
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25 warning('off', 'Octave:assign-as-truth-value');
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26 warning('off', 'Octave:matlab-incompatible');
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27 else
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28 warning('off', 'MATLAB:typeaheadBufferOverflow');
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29 end
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30
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31 %Seperate the Variable Field
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32 if INTERPR
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33 ARGS = strsplit(ARGS,';');
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34 else
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35 ARGS=regexp(ARGS,';','split');
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36 end
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37
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38 %Assign the local variables
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39
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40 %iterate over Fields
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41 for i=1:length(ARGS)
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42 if isempty(ARGS{i})
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43 continue
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44 end
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45 if INTERPR
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46 VALS = strsplit(ARGS{i},':');
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47 else
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48 VALS=regexp(ARGS{i},':','split');
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49 end
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50
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51
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52 if length(VALS)>2
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53 error([" more than one field for variable: " VALS{1} ":" VALS{:} "\n Maybe there are colons in the input argument?"])
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54 end
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55
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56 if strcmp(VALS{1},"RDIFF_RES_DIR"),RDIFF_RES_DIR=VALS{2};continue,end
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57 if strcmp(VALS{1},"RDIFF_INPUT_DIR"),RDIFF_INPUT_DIR=VALS{2};continue,end
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58 if strcmp(VALS{1},"BAM_INPUT1"),BAM_INPUT1=VALS{2};continue,end
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59 if strcmp(VALS{1},"BAM_INPUT2"),BAM_INPUT2=VALS{2};continue,end
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60 if strcmp(VALS{1},"GFF_INPUT"),GFF_INPUT=VALS{2};continue,end
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61 if strcmp(VALS{1},"READ_LENGTH"),READ_LENGTH=str2num(VALS{2});continue,end
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62 if strcmp(VALS{1},"MIN_READ_LENGTH"),MIN_READ_LENGTH=str2num(VALS{2});continue,end
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63 if strcmp(VALS{1},"EST_GENE_EXPR"),EST_GENE_EXPR=str2num(VALS{2});continue,end
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64 if strcmp(VALS{1},"ONLY_GENE_EXPR"),ONLY_GENE_EXPR=str2num(VALS{2});continue,end
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65 if strcmp(VALS{1},"VAR_PATH1"),VAR_PATH1=VALS{2};continue,end
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66 if strcmp(VALS{1},"VAR_PATH2"),VAR_PATH2=VALS{2};continue,end
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67 if strcmp(VALS{1},"SAVE_VAR1"),SAVE_VAR1=VALS{2};continue,end
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68 if strcmp(VALS{1},"SAVE_VAR2"),SAVE_VAR2=VALS{2};continue,end
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69 if strcmp(VALS{1},"PRED_VAR1"),PRED_VAR1=VALS{2};continue,end
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70 if strcmp(VALS{1},"PRED_VAR2"),PRED_VAR2=VALS{2};continue,end
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71 if strcmp(VALS{1},"ONLY_GENE_START"),ONLY_GENE_START=str2num(VALS{2});continue,end
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72 if strcmp(VALS{1},"SUBSAMPLE"),SUBSAMPLE=str2num(VALS{2});continue,end
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73 if strcmp(VALS{1},"CLIP"),CLIP=str2num(VALS{2});continue,end
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74 if strcmp(VALS{1},"BOOTSTRAP"),BOOTSTRAP=str2num(VALS{2});continue,end
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75 if strcmp(VALS{1},"TEST_METH_NAME"),TEST_METH_NAME=VALS{2};continue,end
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76 if strcmp(VALS{1},"MERGE_SAMPLE"),MERGE_SAMPLE=str2num(VALS{2});continue,end
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77 end
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78
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79 %Process Bamfiles
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80 if INTERPR
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81 BAMS1 = strsplit(BAM_INPUT1,',');
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82 BAMS2 = strsplit(BAM_INPUT2,',');
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83 else
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84 BAMS1=regexp(BAM_INPUT1,',','split');
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85 BAMS2=regexp(BAM_INPUT2,',','split');
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86 end
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87
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88 CFG.BAM_FILES={BAMS1{:},BAMS2{:}};
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89
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90 %Name of the experiment. Use the FILENAMES if the entries are empty.
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91 CFG.NAMES=CFG.BAM_FILES;
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92 for i=1:length(CFG.NAMES)
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93 CFG.NAMES{i}=strrep(CFG.NAMES{i},"/","_");
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94 end
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95
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96 % Give the directory where the input-files are
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97 CFG.data_dir = [RDIFF_INPUT_DIR '/'];
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98
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99 % Indicate to which sample the bam-files belong
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100 CFG.SAMPLES=[repmat(1,1,size(BAMS1,2)),repmat(2,1,size(BAMS2,2))];
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101
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102 %Process directories
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103
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104
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105
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106 % Location of the gene structure
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107 CFG.genes_path=GFF_INPUT;
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108
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109 % Output directory
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110
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111 CFG.out_base = [RDIFF_RES_DIR '/'];
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112
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113 % Output directory for temporary files
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114 CFG.out_base_temp = [CFG.out_base '/temp/'];
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115 mkdir(CFG.out_base_temp);
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116
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117
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118 %Check which method to perform
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119 if strcmp(TEST_METH_NAME,'poisson')
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120 CFG.perform_poisson=1;
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121 end
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122 if strcmp(TEST_METH_NAME,'param')
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123 CFG.perform_parametric=1;
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124 end
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125 if strcmp(TEST_METH_NAME,'nonparam')
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126 CFG.perform_nonparametric=1;
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127 end
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128 if strcmp(TEST_METH_NAME,'mmd')
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129 CFG.perform_mmd=1;
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130 end
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131
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132
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133 %Process arguments for gene expression estimation
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134 CFG.estimate_gene_expression=EST_GENE_EXPR;
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135 CFG.only_gene_expression=ONLY_GENE_EXPR;
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136
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137
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138 %Set options for the variance function
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139 CFG.merge_sample1=MERGE_SAMPLE;
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140 CFG.merge_sample2=MERGE_SAMPLE;
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141
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142 %If samples contains leass than one sample, merge replicates
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143 if length(BAMS1)<2
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144 CFG.merge_sample1=1;
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145 end
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146 if length(BAMS2)<2
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147 CFG.merge_sample2=1;
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148 end
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149
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150 %Use predefined parameters
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151 CFG.predefined_variance_function1=[];
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152 if not(isempty(PRED_VAR1))
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153 if INTERPR
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154 VALS = strsplit(PRED_VAR1,',');
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155 else
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156 VALS=regexp(PRED_VAR1,',','split');
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157 end
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158 for i=1:length(VALS)
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159 CFG.predefined_variance_function1(end+1)=str2num(VALS{i});
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160 end
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161 end
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162 CFG.predefined_variance_function2=[];
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163 if not(isempty(PRED_VAR2))
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164 if INTERPR
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165 VALS = strsplit(PRED_VAR2,',');
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166 else
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167 VALS=regexp(PRED_VAR2,',','split');
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168 end
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169 for i=1:length(VALS)
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170 CFG.predefined_variance_function2(end+1)=str2num(VALS{i});
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171 end
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172 end
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173
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174
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175 if not(isempty(SAVE_VAR1))
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176 CFG.save_variance_function_1=SAVE_VAR1;
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177 else
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178 CFG.save_variance_function_1='variance_function_1.mat';
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179 end
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180 if not(isempty(SAVE_VAR2))
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181 CFG.save_variance_function_2=SAVE_VAR2;
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182 else
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183 CFG.save_variance_function_2='variance_function_2.mat';
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184 end
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185
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186 if not(isempty(VAR_PATH1))
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187 CFG.variance_function_1=VAR_PATH1;
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188 end
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189 if not(isempty(VAR_PATH2))
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190 CFG.variance_function_2=VAR_PATH2;
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191 end
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192
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193 %Option not implemented yet
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194 CFG.compute_variance_function_1=1;
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195 CFG.compute_variance_function_2=1;
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196
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197 %use only gene starts and stops for rDiff.nonparametric variance
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198 %function esitmation
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199 CFG.only_gene_start=ONLY_GENE_START;
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200
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201 %Process read arguments
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202 CFG.sequenced_length=READ_LENGTH;
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203 CFG.min_read_length=min(CFG.sequenced_length,MIN_READ_LENGTH);
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204
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205 CFG.rDiff_subsample=SUBSAMPLE;
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206 CFG.rDiff_nonparametric_subsample_variance_estimation=CFG.rDiff_subsample;
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207
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208 CFG.bases_to_clip=CLIP;
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209
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210 %Process arguments for rDiff.nonparametric
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211 CFG.bootstraps=BOOTSTRAP;
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212
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213 return
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