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3
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1 #!/usr/bin/perl
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2
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3 use strict;
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4 use warnings;
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5
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6 my($i, $j, $k);
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7 my $parameters = {};
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8
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9 sub usage {
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10 print "\nUsage: $0 \n\n\t ";
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11 print "REQUIRED \n\t ";
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12 print "-config <config_file> \n\n";
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13 exit(1);
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14 }
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15 if(scalar(@ARGV) == 0){
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16 usage();
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17 }
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18
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19 # Parse the Command Line
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20 &parse_command_line($parameters, @ARGV);
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21
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22 # Log File
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23 my $log_file = $parameters->{config_file} . ".log";
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24 unless ( open(LOG_FILE, ">$log_file") ) {
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25 print "Cannot open file \"$log_file\" to write to!!\n\n";
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26 exit;
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27 }
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28 print LOG_FILE "config = $parameters->{config_file}\n";
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29
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30 # Time Stamp
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31 my $timestamp = localtime(time);
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32 print LOG_FILE $timestamp, "\n";
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33
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34 # Parse Config File
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35 my @samples = ();
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36 my $number_of_samples = &parse_config_file(\@samples, \$parameters);
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37 print LOG_FILE "directory = $parameters->{directory}\n\n";
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38
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39 my $files = {};
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40 # Create Target Regions File
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41 $files->{target_regions_file} = $parameters->{directory} . "/target_regions.dat";
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42 &create_target_regions_file(\$parameters, \$files, \*LOG_FILE);
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43
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44 my @tags = ();
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45 my($reads, $tag);
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46 my($fastq_file_1, $fastq_file_2);
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47 my %proceed = ();
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48 my $alignment_string = '';
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49 my $number_of_alignment_files = 0;
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50 my $cmd = '';
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51
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52 for($i = 0; $i < $number_of_samples; $i++){
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53
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54 # Define Tags
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55 &define_tags(\@samples, \@tags, \$reads, \$tag, \$fastq_file_1, \$fastq_file_2, \$parameters, \*LOG_FILE);
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56
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57 # Check if FASTQ Files Exist and are Non-empty
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58 $proceed{$i} = &decide_to_proceed(\$reads, \$fastq_file_1, \$fastq_file_2);
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59
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60 # Create String of FASTQ Files to be Aligned by bwa_enz
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61 &create_alignment_string($proceed{$i}, \$reads, \$number_of_alignment_files, \$alignment_string, \$fastq_file_1, \$fastq_file_2);
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62 }
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63
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64 # Align the reads with bwa_enz
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65 # Would be better to align paired reads together??
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66 $cmd = &align_reads(\$parameters, $number_of_alignment_files, $alignment_string);
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67 print LOG_FILE $cmd;
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68 system($cmd);
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69
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70 for($i = 0; $i < $number_of_samples; $i++){
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71
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72 # Define Tags
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73 &define_tags(\@samples, \@tags, \$reads, \$tag, \$fastq_file_1, \$fastq_file_2, \$parameters, \*LOG_FILE);
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74
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75 # Define Summary File Names
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76 &define_summary_file_names(\$tag, \$parameters, \$files);
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77
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78 if ( $proceed{$i} == 1 ){
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79
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80 # Convert SAM -> BAM -> BED
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81 &define_alignments_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
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82 $cmd = &rename_sam_files(\$reads, \$files);
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83 $cmd .= &alignments(\$reads, \$fastq_file_1, \$fastq_file_2, \$parameters, \$files);
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84 print LOG_FILE $cmd;
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85 system($cmd);
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86
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87 # De-duplicate the SAM File(s)
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88 &define_de_duplication_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
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89 $cmd = &de_duplication(\$reads, \$fastq_file_1, \$fastq_file_2, \$parameters, \$files);
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90 print LOG_FILE $cmd;
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91 system($cmd);
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92 # What if only reverse read exists? Don't want to de-duplicate?
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93
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94 # Select On-/Off-Target Reads
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95 # Split marked files into two files
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96 &define_on_and_off_target_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
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97 $cmd = &select_on_and_off_target_reads(\$reads, \$parameters, \$files);
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98 print LOG_FILE $cmd;
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99 system($cmd);
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100
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101 # Coverage and Start Sites
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102 &define_coverage_and_start_site_file_names(\$reads, \@tags, \$parameters, \$files);
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103 $cmd = &generate_coverage_and_start_sites(\$reads, \$parameters, \$files);
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104 print LOG_FILE $cmd;
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105 system($cmd);
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106
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107 # Proceed through the rest of the pipeline using the on-target reads
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108
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109 # Create Master Files - one line per read
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110 &define_master_files_file_names(\$reads, \@tags, \$parameters, \$files);
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111 $cmd = &generate_master_files(\$reads, \$parameters, \$files);
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112 print LOG_FILE $cmd;
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113 system($cmd);
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114
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115 # Select Fusion Reads - do not count mapping to a 'novel', i.e., not in refseq, region as a fusion
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116 &define_fusion_reads_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
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117 $cmd = &select_fusion_reads(\$reads, \$parameters, \$files);
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118 print LOG_FILE $cmd;
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119 system($cmd);
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120
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121 # Count Fusions
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122 &define_count_fusions_file_names(\$tag, \$parameters, \$files);
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123 $cmd = &count_fusions(\$reads, \$parameters, \$files);
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124 print LOG_FILE $cmd;
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125 system($cmd);
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126
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127 # Flanking Sequences
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128 &define_flanking_sequences_file_names(\$tag, \$parameters, \$files);
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129 $cmd = &flanking_sequences(\$reads, \$fastq_file_1, \$fastq_file_2, \$parameters, \$files);
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130 print LOG_FILE $cmd;
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131 system($cmd);
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132
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133 # BAM Dedup Files
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134 &define_bam_dedup_files_file_names(\$reads, \@tags, \$parameters, \$files);
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135 $cmd = &bam_dedup_files(\$reads, \$files);
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136 print LOG_FILE $cmd;
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137 system($cmd);
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138
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139 # Consensus Sequences - Fusion and Splice
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140 #&define_consensus_sequences_file_names(\$tag, \$parameters, \$files);
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141 #$cmd = &consensus_sequences(\$reads, \$fastq_file_1, \$fastq_file_2, \$tag, \$parameters, \$files);
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142 #print LOG_FILE $cmd;
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143 #system($cmd);
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144
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145 # Sort SAM Files
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146 &define_sort_sam_files_file_names(\$reads, \@tags, \$parameters, \$files);
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147 $cmd = &sort_sam_files(\$reads, \$files);
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148 print LOG_FILE $cmd;
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149 system($cmd);
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150
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151 # On-target Stats
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152 &define_on_target_stats_file_names(\$tag, \$parameters, \$files);
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153 $cmd = &on_target_stats(\$reads, \$parameters, \$files);
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154 print LOG_FILE $cmd;
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155 system($cmd);
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156
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157 # Total Molecule Counts
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158 &define_total_molecule_counts_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
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159 $cmd = &total_molecule_counts(\$reads, \$parameters, \$files);
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160 print LOG_FILE $cmd;
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161 system($cmd);
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162
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163 # De-duplicated Molecule Counts
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164 &define_de_deduplicated_molecule_counts_file_names(\$reads, \@tags, \$tag, \$parameters, \$files);
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165 $cmd = &de_duplicated_molecule_counts(\$reads, \$parameters, \$files);
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166 print LOG_FILE $cmd;
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167 system($cmd);
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168
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169 # All Molecule Counts
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170 &define_all_molecule_counts_file_names(\$tag, \$parameters, \$files);
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171 $cmd = &all_molecule_counts(\$parameters, \$files);
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172 print LOG_FILE $cmd;
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173 system($cmd);
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174
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175 # QC Check
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176 &define_qc_check_file_names(\$tag, \$parameters, \$files);
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177 $cmd = &qc_check(\$parameters, \$files);
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178 print LOG_FILE $cmd;
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179 system($cmd);
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180
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181 # Coverage Uniformity
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182 &define_coverage_uniformity_file_names(\$tag, \$parameters, \$files);
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183 $cmd = &coverage_uniformity(\$reads, \$parameters, \$files);
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184 print LOG_FILE $cmd;
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185 system($cmd);
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186
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187 # Summary
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188 $cmd = &summary(\$tag, \$parameters, \$files);
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189 print LOG_FILE $cmd;
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190 system($cmd);
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191
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192 # Clean Up
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193 $cmd = &clean_up(\$reads, \$parameters, \$files);
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194 print LOG_FILE $cmd;
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195 system($cmd);
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196 }
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197 else{
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198 # Summary for Unprocessed Sample
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199 $cmd = &summary_for_unprocessed_sample(\$reads, \$fastq_file_1, \$fastq_file_2, \$parameters, \$files);
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200 print LOG_FILE $cmd;
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201 system($cmd);
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202 }
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203
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204 # Time Stamp
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205 $timestamp = localtime(time);
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206 print LOG_FILE $timestamp, "\n";
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207 }
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208
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209 # Join Multiple Samples
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210 #$cmd = &join_multiple_samples(\$parameters);
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211 #print LOG_FILE $cmd;
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212 #system($cmd);
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213
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214 close(LOG_FILE);
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215
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216 exit;
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217
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218 sub parse_command_line {
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219 my($parameters, @ARGV) = @_;
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220 my $next_arg;
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221 while(scalar @ARGV > 0){
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222 $next_arg = shift(@ARGV);
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223 if($next_arg eq "-config"){ $parameters->{config_file} = shift (@ARGV); }
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224 }
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225 }
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226
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227
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228 sub parse_config_file {
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229 my $samples_ref = shift;
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230 my $parameters_ref = shift;
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231 my @values = ();
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232 my $count = 0;
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233 open( FILE, "< $$parameters_ref->{config_file}" ) or die "Can't open $$parameters_ref->{config_file} : $!";
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234 while( <FILE> ) {
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235 chomp;
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236 if ( length($_) > 1 and $_ !~ /^\#/ ){
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237 @values = ();
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238 @values = split(/=/, $_);
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239 if($values[0] eq 'sample'){
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240 @$samples_ref[$count] = $values[1];
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241 $count++;
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242 }
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243 else{
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244 $$parameters_ref->{$values[0]} = $values[1];
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245 }
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246 }
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247 }
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248 my $num_samples = scalar @$samples_ref;
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249 print "number of samples = $num_samples\n";
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250 return $num_samples;
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251 }
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252
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253
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254 sub create_target_regions_file {
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255 my $parameters_ref = shift;
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256 my $files_ref = shift;
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257 my $file_handle_ref = shift;
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258 my $cmd = '';
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259
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260 if ( ($$parameters_ref->{control_regions_file} ne 'NULL') && ($$parameters_ref->{target_regions_file} ne 'NULL') ) {
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261 $cmd = "cat $$parameters_ref->{control_regions_file} $$parameters_ref->{target_regions_file} > $$files_ref->{target_regions_file}\n";
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262 print $file_handle_ref $cmd;
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263 system($cmd);
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264 }
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265 elsif ( $$parameters_ref->{target_regions_file} ne 'NULL' ) {
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266 $$files_ref->{target_regions_file} = $$parameters_ref->{target_regions_file};
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267 }
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268 elsif ( $$parameters_ref->{control_regions_file} ne 'NULL' ) {
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269 $$files_ref->{target_regions_file} = $$parameters_ref->{control_regions_file};
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270 }
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271 else { # Create Target Regions File
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272 my $label;
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273 my $target_file = $$parameters_ref->{directory} . "/target_file.dat";
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274 my $control_file = $$parameters_ref->{directory} . "/control_file.dat";
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275 my $target_temp_outputfile_1 = $$parameters_ref->{directory} . "/target_temp_1.dat";
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276 my $target_temp_outputfile_2 = $$parameters_ref->{directory} . "/target_temp_2.dat";
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277 my $control_temp_outputfile_1 = $$parameters_ref->{directory} . "/control_temp_1.dat";
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278 my $control_temp_outputfile_2 = $$parameters_ref->{directory} . "/control_temp_2.dat";
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279 my $path_to_annotation_script = $$parameters_ref->{path} . "/archer/annotation/";
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280 # Target Primers Fasta File
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281 if ( -e $$parameters_ref->{target_primers} ) {
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282 if ( -s $$parameters_ref->{target_primers} ) {
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283 $label = 'fusion';
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284 $cmd = "$$parameters_ref->{path}/create_target_regions_file.pl -target $$parameters_ref->{target_primers} -label $label -refseq $$parameters_ref->{refseq_file} -gtf_file $$parameters_ref->{gtf_file} -path $path_to_annotation_script -t1 $target_temp_outputfile_1 -t2 $target_temp_outputfile_2 -o $target_file\n";
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285 print $file_handle_ref $cmd;
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286 system($cmd);
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287 }
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288 }
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289 # Control Primers Fasta File
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290 if ( -e $$parameters_ref->{control_primers} ) {
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291 if ( -s $$parameters_ref->{control_primers} ) {
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292 $label = 'housekeeping';
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293 $cmd = "$$parameters_ref->{path}/create_target_regions_file.pl -target $$parameters_ref->{control_primers} -label $label -refseq $$parameters_ref->{refseq_file} -gtf_file $$parameters_ref->{gtf_file} -path $path_to_annotation_script -t1 $control_temp_outputfile_1 -t2 $control_temp_outputfile_2 -o $control_file\n";
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294 print $file_handle_ref $cmd;
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295 system($cmd);
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296 }
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297 }
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298 if ( -e $control_file ) {
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299 if ( -s $control_file ) {
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300 $cmd = "cp $control_file $$files_ref->{target_regions_file}\n";
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301 if ( -e $target_file ) {
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302 if ( -s $target_file ) {
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303 $cmd .= "cat $target_file >> $$files_ref->{target_regions_file}\n";
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304 }
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305 }
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306 print $file_handle_ref $cmd;
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307 system($cmd);
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308 }
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309 }
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310 elsif ( -e $target_file ) {
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311 if ( -s $target_file ) {
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312 $cmd = "cp $target_file $$files_ref->{target_regions_file}\n";
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313 print $file_handle_ref $cmd;
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314 system($cmd);
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315 }
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316 }
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317 $cmd = '';
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318 if ( -e $target_file ) {
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319 $cmd .= "rm $target_temp_outputfile_1\n";
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320 $cmd .= "rm $target_temp_outputfile_2\n";
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321 }
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322 if ( -e $control_file ) {
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323 $cmd .= "rm $control_temp_outputfile_1\n";
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324 $cmd .= "rm $control_temp_outputfile_2\n";
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325 }
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326 print $file_handle_ref $cmd;
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327 system($cmd);
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328
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329 $cmd = '';
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330 if ( -e $target_file ) {
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331 $cmd .= "rm $target_file\n";
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332 }
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333 if ( -e $control_file ) {
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334 $cmd .= "rm $control_file\n";
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335 }
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336 print $file_handle_ref $cmd;
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337 system($cmd);
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338
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339 print $file_handle_ref "\n";
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340 }
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341 }
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342
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343
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344 sub define_tags {
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345 my $samples_array_ref = shift;
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346 my $tags_array_ref = shift;
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347 my $reads_ref = shift;
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348 my $tag_ref = shift;
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349 my $fastq_file_1_ref = shift;
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350 my $fastq_file_2_ref = shift;
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351 my $parameters_ref = shift;
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352 my $file_handle_ref = shift;
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353
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354 @$tags_array_ref = ();
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355 @$tags_array_ref = split(/\s+/, @$samples_array_ref[$i]); # Split samples on whitespace
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356
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357 if( (scalar @$tags_array_ref) == 1 ){
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358 $$reads_ref = 'single';
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359 $$tag_ref = $tags[0];
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360 $$fastq_file_1_ref = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".fastq";
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361 }
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362 else{
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363 $$reads_ref = 'paired';
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364 $$tag_ref = @$tags_array_ref[0] . "_" . @$tags_array_ref[1];
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365 $$fastq_file_1_ref = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".fastq";
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366 $$fastq_file_2_ref = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".fastq";
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367 }
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368
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369 print $$tag_ref, "\n";
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370
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371 print $file_handle_ref $$tag_ref, "\n";
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372 }
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373
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374
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375 sub decide_to_proceed {
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376 my $reads_ref = shift;
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377 my $fastq_file_1_ref = shift;
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378 my $fastq_file_2_ref = shift;
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379 my $proceed = 0;
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380
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381 if ( $$reads_ref eq 'single' ) {
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382 if ( -e $$fastq_file_1_ref ) {
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383 if ( -s $$fastq_file_1_ref ) {
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384 $proceed = 1;
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385 }
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386 }
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387 else{
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388 $$fastq_file_1_ref .= ".gz"; # See if fastq_file_1 exists in gzipped form
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389 if ( -e $$fastq_file_1_ref ) {
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390 if ( -s $$fastq_file_1_ref ) {
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391 $proceed = 1;
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392 }
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393 }
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394 }
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395 }
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396 if ( $$reads_ref eq 'paired' ) {
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397 if ( -e $$fastq_file_1_ref ) {
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398 if ( -s $$fastq_file_1_ref ) {
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399 if ( -e $$fastq_file_2_ref ) {
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400 if ( -s $$fastq_file_2_ref ) {
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401 $proceed = 1;
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402 }
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403 }
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404 else{
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405 $$fastq_file_2_ref .= ".gz"; # See if fastq_file_2 exists in gzipped form
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406 if ( -e $$fastq_file_2_ref ) {
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407 if ( -s $$fastq_file_2_ref ) {
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408 $proceed = 1;
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409 }
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410 }
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411 }
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412 }
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413 }
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414 else{
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415 $$fastq_file_1_ref .= ".gz"; # See if fastq_file_1 exists in gzipped form
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416 if ( -e $$fastq_file_1_ref ) {
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417 if ( -s $$fastq_file_1_ref ) {
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418 if ( -e $$fastq_file_2_ref ) {
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419 if ( -s $$fastq_file_2_ref ) {
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420 $proceed = 1;
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421 }
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422 }
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423 else{
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424 $$fastq_file_2_ref .= ".gz"; # See if fastq_file_2 exists in gzipped form
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|
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425 if ( -e $$fastq_file_2_ref ) {
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|
426 if ( -s $$fastq_file_2_ref ) {
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427 $proceed = 1;
|
|
|
428 }
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429 }
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430 }
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431 }
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432 }
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433 }
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|
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434 }
|
|
|
435 return $proceed;
|
|
|
436 }
|
|
|
437
|
|
|
438
|
|
|
439 sub create_alignment_string {
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|
440 my $proceed_value = shift;
|
|
|
441 my $reads_ref = shift;
|
|
|
442 my $number_of_alignment_files_ref = shift;
|
|
|
443 my $alignment_string_ref = shift;
|
|
|
444 my $fastq_file_1_ref = shift;
|
|
|
445 my $fastq_file_2_ref = shift;
|
|
|
446
|
|
|
447 if ( $proceed_value == 1 ) {
|
|
|
448 if ( $$number_of_alignment_files_ref == 0 ){
|
|
|
449 $$alignment_string_ref = $$fastq_file_1_ref;
|
|
|
450 }
|
|
|
451 else {
|
|
|
452 $$alignment_string_ref .= " " . $$fastq_file_1_ref;
|
|
|
453 }
|
|
|
454 $$number_of_alignment_files_ref++;
|
|
|
455 if ( $$reads_ref eq 'paired' ) {
|
|
|
456 $$alignment_string_ref .= " " . $$fastq_file_2_ref;
|
|
|
457 $$number_of_alignment_files_ref++;
|
|
|
458 }
|
|
|
459 }
|
|
|
460 }
|
|
|
461
|
|
|
462
|
|
|
463 sub align_reads {
|
|
|
464 my $parameters_ref = shift;
|
|
|
465 my $number_of_alignment_files_value = shift;
|
|
|
466 my $alignment_string_value = shift;
|
|
|
467 my $cmd_line = "echo Align Reads\n";
|
|
|
468 if ( $number_of_alignment_files_value > 0 ) {
|
|
|
469 $cmd_line .= "bwa_enz mem -Q 0 -m -D $$parameters_ref->{directory} $$parameters_ref->{reference_file} $alignment_string_value\n";
|
|
|
470 }
|
|
|
471 return $cmd_line;
|
|
|
472 }
|
|
|
473
|
|
|
474
|
|
|
475 sub rename_sam_files {
|
|
|
476 my $reads_ref = shift;
|
|
|
477 my $files_ref = shift;
|
|
|
478 my $cmd_line = "echo Rename SAM Files\n";
|
|
|
479 $cmd_line .= "mv $$files_ref->{sam_file_1_orig} $$files_ref->{sam_file_1_full}\n";
|
|
|
480 if ( $$reads_ref eq 'paired' ) {
|
|
|
481 $cmd_line .= "mv $$files_ref->{sam_file_2_orig} $$files_ref->{sam_file_2_full}\n";
|
|
|
482 }
|
|
|
483 return $cmd_line;
|
|
|
484 }
|
|
|
485
|
|
|
486
|
|
|
487 sub alignments {
|
|
|
488 my $reads_ref = shift;
|
|
|
489 my $fastq_file_1_ref = shift;
|
|
|
490 my $fastq_file_2_ref = shift;
|
|
|
491 my $parameters_ref = shift;
|
|
|
492 my $files_ref = shift;
|
|
|
493 my $cmd_line = "echo Alignments\n";
|
|
|
494
|
|
|
495 # -S input is SAM
|
|
|
496 # -b output is BAM
|
|
|
497 # -h print header for the SAM output
|
|
|
498
|
|
|
499 # $cmd_line .= "bwa mem $$parameters_ref->{reference_file} $$fastq_file_1_ref > $$files_ref->{sam_file_1_full}\n";
|
|
|
500 $cmd_line .= "samtools view -Shq 40 $$files_ref->{sam_file_1_full} > $$files_ref->{sam_file_1}\n";
|
|
|
501 $cmd_line .= "samtools view -bS $$files_ref->{sam_file_1} > $$files_ref->{bam_file_1}\n";
|
|
|
502 $cmd_line .= "bamToBed -i $$files_ref->{bam_file_1} > $$files_ref->{bed_file_1_orig}\n";
|
|
|
503 if ( $$reads_ref eq 'single' ) {
|
|
|
504 $cmd_line .= "mv $$files_ref->{bed_file_1_orig} $$files_ref->{bed_file_combined}\n";
|
|
|
505 }
|
|
|
506 elsif ( $$reads_ref eq 'paired' ) {
|
|
|
507 # $cmd_line .= "bwa mem $$parameters_ref->{reference_file} $$fastq_file_2_ref > $$files_ref->{sam_file_2_full}\n";
|
|
|
508 $cmd_line .= "samtools view -Shq 40 $$files_ref->{sam_file_2_full} > $$files_ref->{sam_file_2}\n";
|
|
|
509 $cmd_line .= "samtools view -bS $$files_ref->{sam_file_2} > $$files_ref->{bam_file_2}\n";
|
|
|
510 $cmd_line .= "bamToBed -i $$files_ref->{bam_file_2} > $$files_ref->{bed_file_2_orig}\n";
|
|
|
511 $cmd_line .= "cat $$files_ref->{bed_file_1_orig} $$files_ref->{bed_file_2_orig} > $$files_ref->{bed_file_combined}\n";
|
|
|
512 $cmd_line .= "rm $$files_ref->{bed_file_1_orig}\n";
|
|
|
513 $cmd_line .= "rm $$files_ref->{bed_file_2_orig}\n";
|
|
|
514 }
|
|
|
515 return $cmd_line;
|
|
|
516 }
|
|
|
517
|
|
|
518
|
|
|
519 sub de_duplication {
|
|
|
520 my $reads_ref = shift;
|
|
|
521 my $fastq_file_1_ref = shift;
|
|
|
522 my $fastq_file_2_ref = shift;
|
|
|
523 my $parameters_ref = shift;
|
|
|
524 my $files_ref = shift;
|
|
|
525 my $cmd_line = "echo De-duplication\n";
|
|
|
526
|
|
|
527 if ( $$reads_ref eq 'single' ) {
|
|
|
528 $cmd_line .= "sort -k4,4 $$files_ref->{bed_file_combined}|$$parameters_ref->{path}/dedup_pipeline.sh -p $$parameters_ref->{path} -b /dev/stdin -f $$fastq_file_1_ref > $$files_ref->{dedup_file}\n";
|
|
|
529 }
|
|
|
530 else{
|
|
|
531 $cmd_line .= "sort -k4,4 $$files_ref->{bed_file_combined}|$$parameters_ref->{path}/dedup_pipeline.sh -p $$parameters_ref->{path} -b /dev/stdin -f $$fastq_file_1_ref -2 $$fastq_file_2_ref > $$files_ref->{dedup_file}\n";
|
|
|
532 }
|
|
|
533 $cmd_line .= "$$parameters_ref->{path}/de_dup_2_hash.pl -dedup $$files_ref->{dedup_file} -sam $$files_ref->{sam_file_1} -o $$files_ref->{sam_dedup_file_1}\n";
|
|
|
534 $cmd_line .= "$$parameters_ref->{path}/de_dup_2_hash.pl -dedup $$files_ref->{dedup_file} -sam $$files_ref->{sam_file_1_full} -o $$files_ref->{sam_dedup_file_1_full}\n";
|
|
|
535 if ( $$reads_ref eq 'paired' ) {
|
|
|
536 $cmd_line .= "$$parameters_ref->{path}/de_dup_2_hash.pl -dedup $$files_ref->{dedup_file} -sam $$files_ref->{sam_file_2} -o $$files_ref->{sam_dedup_file_2}\n";
|
|
|
537 $cmd_line .= "$$parameters_ref->{path}/de_dup_2_hash.pl -dedup $$files_ref->{dedup_file} -sam $$files_ref->{sam_file_2_full} -o $$files_ref->{sam_dedup_file_2_full}\n";
|
|
|
538 }
|
|
|
539 return $cmd_line;
|
|
|
540 }
|
|
|
541
|
|
|
542
|
|
|
543 sub select_on_and_off_target_reads {
|
|
|
544 my $reads_ref = shift;
|
|
|
545 my $parameters_ref = shift;
|
|
|
546 my $files_ref = shift;
|
|
|
547 my $cmd_line = "echo Select On- and Off-target Reads\n";
|
|
|
548
|
|
|
549 # Create BED file of target regions
|
|
|
550 $cmd_line .= "$$parameters_ref->{path}/convert_target_regions_to_bed.pl -t $$files_ref->{target_regions_file} -o $$files_ref->{target_regions_bed_file}\n";
|
|
|
551
|
|
|
552 # All Reads
|
|
|
553 # Create a master file from the SAM file
|
|
|
554 # Join the master file
|
|
|
555 # Select the appropriate segment for each read id and create a BED file - need to have only one entry for each read in the BED file
|
|
|
556 # Convert BED files of reads to single points - do this so that only start of R2 and end of R1 are counted in overlapping with the target regions so that only the target region that overlaps with these end points will be counted as being hit - assumes that there are no overlapping regions in the target regions file
|
|
|
557 # Get intersection of reads with target regions
|
|
|
558 $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_file_1} -o $$files_ref->{full_master_prejoin_file_1}\n";
|
|
|
559 $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{full_master_prejoin_file_1} -o $$files_ref->{full_master_file_1}\n";
|
|
|
560 $cmd_line .= "$$parameters_ref->{path}/convert_master_file_to_bed.pl -master $$files_ref->{full_master_file_1} -read $$reads_ref -tag 1 -o $$files_ref->{bed_file_1}\n";
|
|
|
561 $cmd_line .= "$$parameters_ref->{path}/convert_bed_to_single_points.pl -b $$files_ref->{bed_file_1} -read $$reads_ref -tag 1 -o $$files_ref->{bed_points_file_1}\n";
|
|
|
562 $cmd_line .= "intersectBed -a $$files_ref->{target_regions_bed_file} -b $$files_ref->{bed_points_file_1} -wa -wb > $$files_ref->{intersect_file_1}\n";
|
|
|
563 if ( $$reads_ref eq 'paired' ) {
|
|
|
564 $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_file_2} -o $$files_ref->{full_master_prejoin_file_2}\n";
|
|
|
565 $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{full_master_prejoin_file_2} -o $$files_ref->{full_master_file_2}\n";
|
|
|
566 $cmd_line .= "$$parameters_ref->{path}/convert_master_file_to_bed.pl -master $$files_ref->{full_master_file_2} -read $$reads_ref -tag 2 -o $$files_ref->{bed_file_2}\n";
|
|
|
567 $cmd_line .= "$$parameters_ref->{path}/convert_bed_to_single_points.pl -b $$files_ref->{bed_file_2} -read $$reads_ref -tag 2 -o $$files_ref->{bed_points_file_2}\n";
|
|
|
568 $cmd_line .= "intersectBed -a $$files_ref->{target_regions_bed_file} -b $$files_ref->{bed_points_file_2} -wa -wb > $$files_ref->{intersect_file_2}\n";
|
|
|
569 $cmd_line .= "cat $$files_ref->{intersect_file_1} $$files_ref->{intersect_file_2} > $$files_ref->{intersect_file_combined}\n";
|
|
|
570 }
|
|
|
571 # Create SAM files of the on- and off-target reads. On-target files contain all reads in which at least one of R1/R2 is on-target. Off-target files contain the remaining reads.
|
|
|
572 # On-/Off-target Alone Read 1
|
|
|
573 $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_file_1} -i $$files_ref->{intersect_file_1} -on $$files_ref->{sam_on_target_alone_file_1}\n";
|
|
|
574 $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_file_1} -on $$files_ref->{sam_on_target_alone_file_1} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_file_1_marked}\n";
|
|
|
575 $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_file_1_marked} > $$files_ref->{sam_off_target_alone_file_1}\n";
|
|
|
576 if ( $$reads_ref eq 'paired' ) {
|
|
|
577 # On-/Off-target Alone Read 2
|
|
|
578 $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_file_2} -i $$files_ref->{intersect_file_2} -on $$files_ref->{sam_on_target_alone_file_2}\n";
|
|
|
579 $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_file_2} -on $$files_ref->{sam_on_target_alone_file_2} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_file_2_marked}\n";
|
|
|
580 $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_file_2_marked} > $$files_ref->{sam_off_target_alone_file_2}\n";
|
|
|
581 # On-/Off-target Either Read 1
|
|
|
582 $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_file_1} -i $$files_ref->{intersect_file_combined} -on $$files_ref->{sam_on_target_file_1}\n";
|
|
|
583 $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_file_1} -on $$files_ref->{sam_on_target_file_1} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_file_1_marked}\n";
|
|
|
584 $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_file_1_marked} > $$files_ref->{sam_off_target_file_1}\n";
|
|
|
585 # On-/Off-target Either Read 2
|
|
|
586 $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_file_2} -i $$files_ref->{intersect_file_combined} -on $$files_ref->{sam_on_target_file_2}\n";
|
|
|
587 $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_file_2} -on $$files_ref->{sam_on_target_file_2} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_file_2_marked}\n";
|
|
|
588 $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_file_2_marked} > $$files_ref->{sam_off_target_file_2}\n";
|
|
|
589 }
|
|
|
590
|
|
|
591 # De-duplicated Reads
|
|
|
592 $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_file_1} -o $$files_ref->{full_master_dedup_prejoin_file_1}\n";
|
|
|
593 $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{full_master_dedup_prejoin_file_1} -o $$files_ref->{full_master_dedup_file_1}\n";
|
|
|
594 $cmd_line .= "$$parameters_ref->{path}/convert_master_file_to_bed.pl -master $$files_ref->{full_master_dedup_file_1} -read $$reads_ref -tag 1 -o $$files_ref->{bed_dedup_file_1}\n";
|
|
|
595 $cmd_line .= "$$parameters_ref->{path}/convert_bed_to_single_points.pl -b $$files_ref->{bed_dedup_file_1} -read $$reads_ref -tag 1 -o $$files_ref->{bed_points_dedup_file_1}\n";
|
|
|
596 $cmd_line .= "intersectBed -a $$files_ref->{target_regions_bed_file} -b $$files_ref->{bed_points_dedup_file_1} -wa -wb > $$files_ref->{intersect_dedup_file_1}\n";
|
|
|
597 if ( $$reads_ref eq 'paired' ) {
|
|
|
598 $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_file_2} -o $$files_ref->{full_master_dedup_prejoin_file_2}\n";
|
|
|
599 $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{full_master_dedup_prejoin_file_2} -o $$files_ref->{full_master_dedup_file_2}\n";
|
|
|
600 $cmd_line .= "$$parameters_ref->{path}/convert_master_file_to_bed.pl -master $$files_ref->{full_master_dedup_file_2} -read $$reads_ref -tag 2 -o $$files_ref->{bed_dedup_file_2}\n";
|
|
|
601 $cmd_line .= "$$parameters_ref->{path}/convert_bed_to_single_points.pl -b $$files_ref->{bed_dedup_file_2} -read $$reads_ref -tag 2 -o $$files_ref->{bed_points_dedup_file_2}\n";
|
|
|
602 $cmd_line .= "intersectBed -a $$files_ref->{target_regions_bed_file} -b $$files_ref->{bed_points_dedup_file_2} -wa -wb > $$files_ref->{intersect_dedup_file_2}\n";
|
|
|
603 $cmd_line .= "cat $$files_ref->{intersect_dedup_file_1} $$files_ref->{intersect_dedup_file_2} > $$files_ref->{intersect_dedup_file_combined}\n";
|
|
|
604 }
|
|
|
605 # Create SAM files of the on- and off-target reads. On-target files contain all reads in which at least one of R1/R2 is on-target. Off-target files contain the remaining reads.
|
|
|
606 # On-/Off-target Alone Read 1
|
|
|
607 $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_dedup_file_1} -i $$files_ref->{intersect_dedup_file_1} -on $$files_ref->{sam_dedup_on_target_alone_file_1}\n";
|
|
|
608 $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_dedup_file_1} -on $$files_ref->{sam_dedup_on_target_alone_file_1} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_dedup_file_1_marked}\n";
|
|
|
609 $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_dedup_file_1_marked} > $$files_ref->{sam_dedup_off_target_alone_file_1}\n";
|
|
|
610 if ( $$reads_ref eq 'paired' ) {
|
|
|
611 # On-/Off-target Alone Read 2
|
|
|
612 $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_dedup_file_2} -i $$files_ref->{intersect_dedup_file_2} -on $$files_ref->{sam_dedup_on_target_alone_file_2}\n";
|
|
|
613 $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_dedup_file_2} -on $$files_ref->{sam_dedup_on_target_alone_file_2} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_dedup_file_2_marked}\n";
|
|
|
614 $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_dedup_file_2_marked} > $$files_ref->{sam_dedup_off_target_alone_file_2}\n";
|
|
|
615 # On-/Off-target Either Read 1
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|
616 $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_dedup_file_1} -i $$files_ref->{intersect_dedup_file_combined} -on $$files_ref->{sam_dedup_on_target_file_1}\n";
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|
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617 $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_dedup_file_1} -on $$files_ref->{sam_dedup_on_target_file_1} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_dedup_file_1_marked}\n";
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|
|
618 $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_dedup_file_1_marked} > $$files_ref->{sam_dedup_off_target_file_1}\n";
|
|
|
619 # On-/Off-target Either Read 2
|
|
|
620 $cmd_line .= "$$parameters_ref->{path}/generate_on_target_sam_files_hash.pl -sam $$files_ref->{sam_dedup_file_2} -i $$files_ref->{intersect_dedup_file_combined} -on $$files_ref->{sam_dedup_on_target_file_2}\n";
|
|
|
621 $cmd_line .= "$$parameters_ref->{path}/mark_on_target_reads.pl -sam $$files_ref->{sam_dedup_file_2} -on $$files_ref->{sam_dedup_on_target_file_2} -temp_dir $$parameters_ref->{directory} -o $$files_ref->{sam_dedup_file_2_marked}\n";
|
|
|
622 $cmd_line .= "grep -v 'ON_TARGET' $$files_ref->{sam_dedup_file_2_marked} > $$files_ref->{sam_dedup_off_target_file_2}\n";
|
|
|
623 }
|
|
|
624 return $cmd_line;
|
|
|
625 }
|
|
|
626
|
|
|
627
|
|
|
628 sub generate_coverage_and_start_sites {
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|
|
629 my $reads_ref = shift;
|
|
|
630 my $parameters_ref = shift;
|
|
|
631 my $files_ref = shift;
|
|
|
632 my $cmd_line = "echo Generate Coverage and Start Sites\n";
|
|
|
633
|
|
|
634 $cmd_line .= "bash $$parameters_ref->{path}/generateHistAndStartSiteInfo.sh $$files_ref->{sam_dedup_file_1} $$parameters_ref->{reference_file} $$parameters_ref->{reference_file_index} $$files_ref->{start_site_dedup_file_1} $$files_ref->{coverage_dedup_file_1} $$parameters_ref->{path}\n";
|
|
|
635
|
|
|
636 if ( $$reads_ref eq 'paired' ) {
|
|
|
637 $cmd_line .= "bash $$parameters_ref->{path}/generateHistAndStartSiteInfo.sh $$files_ref->{sam_dedup_file_2} $$parameters_ref->{reference_file} $$parameters_ref->{reference_file_index} $$files_ref->{start_site_dedup_file_2} $$files_ref->{coverage_dedup_file_2} $$parameters_ref->{path}\n";
|
|
|
638 }
|
|
|
639
|
|
|
640 return $cmd_line;
|
|
|
641 }
|
|
|
642
|
|
|
643
|
|
|
644 sub generate_master_files {
|
|
|
645 my $reads_ref = shift;
|
|
|
646 my $parameters_ref = shift;
|
|
|
647 my $files_ref = shift;
|
|
|
648 my $cmd_line = "echo Generate Master Files\n";
|
|
|
649
|
|
|
650 # Create a master file of all reads with one line per read
|
|
|
651 if ( $$reads_ref eq 'single' ) {
|
|
|
652 $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_on_target_alone_file_1} -o $$files_ref->{master_dedup_no_annotation_file_1}\n";
|
|
|
653 }
|
|
|
654 else{
|
|
|
655 $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_on_target_file_1} -o $$files_ref->{master_dedup_no_annotation_file_1}\n";
|
|
|
656 }
|
|
|
657
|
|
|
658 $cmd_line .= "python $$parameters_ref->{path}/archer/annotation/annotate.py --gtf_file $$parameters_ref->{gtf_file} --coordinate_file $$files_ref->{master_dedup_no_annotation_file_1} --outfile $$files_ref->{master_dedup_prejoin_file_1} --chromosome_indices 1,1 --coordinate_indices 5,6\n";
|
|
|
659
|
|
|
660 $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{master_dedup_prejoin_file_1} -o $$files_ref->{master_dedup_file_1}\n";
|
|
|
661
|
|
|
662 if ( $$reads_ref eq 'paired' ) {
|
|
|
663 $cmd_line .= "$$parameters_ref->{path}/generate_master_file_without_annotation.pl -sam $$files_ref->{sam_dedup_on_target_file_2} -o $$files_ref->{master_dedup_no_annotation_file_2}\n";
|
|
|
664
|
|
|
665 $cmd_line .= "python $$parameters_ref->{path}/archer/annotation/annotate.py --gtf_file $$parameters_ref->{gtf_file} --coordinate_file $$files_ref->{master_dedup_no_annotation_file_2} --outfile $$files_ref->{master_dedup_prejoin_file_2} --chromosome_indices 1,1 --coordinate_indices 5,6\n";
|
|
|
666
|
|
|
667 $cmd_line .= "$$parameters_ref->{path}/join_master_file.pl -master $$files_ref->{master_dedup_prejoin_file_2} -o $$files_ref->{master_dedup_file_2}\n";
|
|
|
668 }
|
|
|
669
|
|
|
670 return $cmd_line;
|
|
|
671 }
|
|
|
672
|
|
|
673 sub select_fusion_reads {
|
|
|
674 my $reads_ref = shift;
|
|
|
675 my $parameters_ref = shift;
|
|
|
676 my $files_ref = shift;
|
|
|
677 my $cmd_line = "echo Select Fusion Reads\n";
|
|
|
678
|
|
|
679 $cmd_line .= "$$parameters_ref->{path}/select_fusion_reads.pl -master $$files_ref->{master_dedup_file_1} -tag 1 -o1 $$files_ref->{one_segment_reads_file_1} -os $$files_ref->{splice_reads_file_1} -of $$files_ref->{fusion_reads_file_1} -omf $$files_ref->{multi_fusion_reads_file_1}\n";
|
|
|
680
|
|
|
681 if ( $$reads_ref eq 'single' ) {
|
|
|
682 $cmd_line .= "cp $$files_ref->{fusion_reads_file_1} $$files_ref->{fusion_reads_file}\n";
|
|
|
683 $cmd_line .= "cp $$files_ref->{splice_reads_file_1} $$files_ref->{splice_reads_file}\n";
|
|
|
684 }
|
|
|
685
|
|
|
686 if ( $$reads_ref eq 'paired' ) {
|
|
|
687 $cmd_line .= "$$parameters_ref->{path}/select_fusion_reads.pl -master $$files_ref->{master_dedup_file_2} -tag 2 -o1 $$files_ref->{one_segment_reads_file_2} -os $$files_ref->{splice_reads_file_2} -of $$files_ref->{fusion_reads_file_2} -omf $$files_ref->{multi_fusion_reads_file_2}\n";
|
|
|
688 $cmd_line .= "cat $$files_ref->{fusion_reads_file_1} $$files_ref->{fusion_reads_file_2} > $$files_ref->{fusion_reads_file}\n";
|
|
|
689 $cmd_line .= "cat $$files_ref->{splice_reads_file_1} $$files_ref->{splice_reads_file_2} > $$files_ref->{splice_reads_file}\n";
|
|
|
690 }
|
|
|
691
|
|
|
692 return $cmd_line;
|
|
|
693 }
|
|
|
694
|
|
|
695 sub count_fusions {
|
|
|
696 my $reads_ref = shift;
|
|
|
697 my $parameters_ref = shift;
|
|
|
698 my $files_ref = shift;
|
|
|
699 my $cmd_line = "echo Count Fusions and Splice Events\n";
|
|
|
700
|
|
|
701 # Count the number of each type of fusion pair, i.e., Gene A Exon X with Gene B Exon Y, get the median value of the coordinate of each breakpoint, sort and output each type
|
|
|
702 $cmd_line .= "$$parameters_ref->{path}/count_fusions.pl -t $$files_ref->{target_regions_file} -fr $$files_ref->{fusion_reads_file} -min 30 -gtf $$parameters_ref->{gtf_file} -read $$reads_ref -limit 10 -min_occ 5 -ob $$files_ref->{fusion_counts_bare_file} -o $$files_ref->{fusion_counts_file}\n";
|
|
|
703
|
|
|
704 # Count the number of each type of splice pair - Use default values for -limit and -min_occ so that all splices will be reported
|
|
|
705 $cmd_line .= "$$parameters_ref->{path}/count_fusions.pl -t $$files_ref->{target_regions_file} -fr $$files_ref->{splice_reads_file} -min 30 -gtf $$parameters_ref->{gtf_file} -read $$reads_ref -ob $$files_ref->{splice_counts_bare_file} -o $$files_ref->{splice_counts_file}\n";
|
|
|
706
|
|
|
707 # Add splice evidence to fusion counts
|
|
|
708 $cmd_line .= "$$parameters_ref->{path}/add_splice_to_fusion_counts.pl -fcb $$files_ref->{fusion_counts_bare_file} -scb $$files_ref->{splice_counts_bare_file} -o $$files_ref->{fusion_counts_with_splice_bare_file} -om $$files_ref->{fusion_counts_with_splice_bare_file_machine}\n";
|
|
|
709
|
|
|
710 return $cmd_line;
|
|
|
711 }
|
|
|
712
|
|
|
713
|
|
|
714 sub flanking_sequences {
|
|
|
715 my $reads_ref = shift;
|
|
|
716 my $fastq_file_1_ref = shift;
|
|
|
717 my $fastq_file_2_ref = shift;
|
|
|
718 my $parameters_ref = shift;
|
|
|
719 my $files_ref = shift;
|
|
|
720 my $cmd_line = "echo Flanking Sequences\n";
|
|
|
721
|
|
|
722 if ( $$reads_ref eq 'single' ) {
|
|
|
723 $cmd_line .= "$$parameters_ref->{path}/flanking_sequences.pl -fcb $$files_ref->{fusion_counts_bare_file} -fr $$files_ref->{fusion_reads_file} -read $$reads_ref -fastq_1 $$fastq_file_1_ref -o $$files_ref->{flanking_sequences_file}\n";
|
|
|
724 $cmd_line .= "$$parameters_ref->{path}/flanking_sequences.pl -fcb $$files_ref->{splice_counts_bare_file} -fr $$files_ref->{splice_reads_file} -read $$reads_ref -fastq_1 $$fastq_file_1_ref -o $$files_ref->{flanking_splice_sequences_file}\n";
|
|
|
725 }
|
|
|
726 else{
|
|
|
727 $cmd_line .= "$$parameters_ref->{path}/flanking_sequences.pl -fcb $$files_ref->{fusion_counts_bare_file} -fr $$files_ref->{fusion_reads_file} -read $$reads_ref -fastq_1 $$fastq_file_1_ref -fastq_2 $$fastq_file_2_ref -o $$files_ref->{flanking_sequences_file}\n";
|
|
|
728 $cmd_line .= "$$parameters_ref->{path}/flanking_sequences.pl -fcb $$files_ref->{splice_counts_bare_file} -fr $$files_ref->{splice_reads_file} -read $$reads_ref -fastq_1 $$fastq_file_1_ref -fastq_2 $$fastq_file_2_ref -o $$files_ref->{flanking_splice_sequences_file}\n";
|
|
|
729 }
|
|
|
730 return $cmd_line;
|
|
|
731 }
|
|
|
732
|
|
|
733
|
|
|
734 sub bam_dedup_files {
|
|
|
735 my $reads_ref = shift;
|
|
|
736 my $files_ref = shift;
|
|
|
737 my $cmd_line = "echo BAM Dedup Files\n";
|
|
|
738 # Make sorted de-dup BAM files
|
|
|
739 $cmd_line .= "samtools view -bS $$files_ref->{sam_dedup_file_1} > $$files_ref->{bam_dedup_file_1}\n";
|
|
|
740 $cmd_line .= "samtools sort $$files_ref->{bam_dedup_file_1} $$files_ref->{bam_dedup_sorted_file_1_name}\n";
|
|
|
741 $cmd_line .= "samtools index $$files_ref->{bam_dedup_sorted_file_1}\n";
|
|
|
742 if ( $$reads_ref eq 'paired' ) {
|
|
|
743 $cmd_line .= "samtools view -bS $$files_ref->{sam_dedup_file_2} > $$files_ref->{bam_dedup_file_2}\n";
|
|
|
744 $cmd_line .= "samtools sort $$files_ref->{bam_dedup_file_2} $$files_ref->{bam_dedup_sorted_file_2_name}\n";
|
|
|
745 $cmd_line .= "samtools index $$files_ref->{bam_dedup_sorted_file_2}\n";
|
|
|
746 }
|
|
|
747 return $cmd_line;
|
|
|
748 }
|
|
|
749
|
|
|
750
|
|
|
751 sub consensus_sequences {
|
|
|
752 my $reads_ref = shift;
|
|
|
753 my $fastq_file_1_ref = shift;
|
|
|
754 my $fastq_file_2_ref = shift;
|
|
|
755 my $tag_ref = shift;
|
|
|
756 my $parameters_ref = shift;
|
|
|
757 my $files_ref = shift;
|
|
|
758 my $cmd_line = "echo Consensus Sequences\n";
|
|
|
759
|
|
|
760 # Fusion and Splice Consensus Sequences
|
|
|
761 if ( $$reads_ref eq 'single' ) {
|
|
|
762 $cmd_line .= "bash $$parameters_ref->{path}/consensus_pipeline/batch_pipeline.sh -1 $$files_ref->{bam_dedup_sorted_file_1} -a $$fastq_file_1_ref -f $$parameters_ref->{reference_file} -r $$files_ref->{flanking_sequences_file} -d $$parameters_ref->{path}/consensus_pipeline/ -s $$files_ref->{consensus_fusion_std_out_file} -e $$files_ref->{consensus_fusion_std_err_file}\n";
|
|
|
763 $cmd_line .= "bash $$parameters_ref->{path}/consensus_pipeline/batch_pipeline.sh -1 $$files_ref->{bam_dedup_sorted_file_1} -a $$fastq_file_1_ref -f $$parameters_ref->{reference_file} -r $$files_ref->{flanking_splice_sequences_file} -d $$parameters_ref->{path}/consensus_pipeline/ -s $$files_ref->{consensus_splice_std_out_file} -e $$files_ref->{consensus_splice_std_err_file}\n";
|
|
|
764 }
|
|
|
765 else{
|
|
|
766 $cmd_line .= "bash $$parameters_ref->{path}/consensus_pipeline/batch_pipeline.sh -1 $$files_ref->{bam_dedup_sorted_file_1} -2 $$files_ref->{bam_dedup_sorted_file_2} -a $$fastq_file_1_ref -b $$fastq_file_2_ref -f $$parameters_ref->{reference_file} -r $$files_ref->{flanking_sequences_file} -d $$parameters_ref->{path}/consensus_pipeline/ -s $$files_ref->{consensus_fusion_std_out_file} -e $$files_ref->{consensus_fusion_std_err_file}\n";
|
|
|
767 $cmd_line .= "bash $$parameters_ref->{path}/consensus_pipeline/batch_pipeline.sh -1 $$files_ref->{bam_dedup_sorted_file_1} -2 $$files_ref->{bam_dedup_sorted_file_2} -a $$fastq_file_1_ref -b $$fastq_file_2_ref -f $$parameters_ref->{reference_file} -r $$files_ref->{flanking_splice_sequences_file} -d $$parameters_ref->{path}/consensus_pipeline/ -s $$files_ref->{consensus_splice_std_out_file} -e $$files_ref->{consensus_splice_std_err_file}\n";
|
|
|
768 }
|
|
|
769
|
|
|
770 # Pair Fusion Candidates with Splice Sequences
|
|
|
771 $cmd_line .= "$$parameters_ref->{path}/pair_fusion_and_splice_sequences.pl -fc $$files_ref->{fusion_counts_bare_file} -sc $$files_ref->{splice_counts_bare_file} -tag $$tag_ref -o $$files_ref->{fusion_and_splice_consensus_file}\n";
|
|
|
772
|
|
|
773 return $cmd_line;
|
|
|
774 }
|
|
|
775
|
|
|
776
|
|
|
777 sub sort_sam_files {
|
|
|
778 my $reads_ref = shift;
|
|
|
779 my $files_ref = shift;
|
|
|
780 my $cmd_line = "echo Sort SAM Files\n";
|
|
|
781
|
|
|
782 $cmd_line .= "sort -k1,1 $$files_ref->{sam_on_target_alone_file_1} > $$files_ref->{sam_on_target_alone_file_1_linux_sorted}\n";
|
|
|
783 $cmd_line .= "sort -k1,1 $$files_ref->{sam_off_target_alone_file_1} > $$files_ref->{sam_off_target_alone_file_1_linux_sorted}\n";
|
|
|
784 $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_on_target_alone_file_1} > $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted}\n";
|
|
|
785 $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_off_target_alone_file_1} > $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted}\n";
|
|
|
786
|
|
|
787 $cmd_line .= "samtools view -bS $$files_ref->{sam_file_1_full} > $$files_ref->{bam_file_1_full}\n";
|
|
|
788 $cmd_line .= "samtools sort -n $$files_ref->{bam_file_1_full} $$files_ref->{bam_file_1_full_prefix}\n";
|
|
|
789 $cmd_line .= "samtools view -h $$files_ref->{bam_file_1_full_sorted} > $$files_ref->{sam_file_1_full_sorted}\n";
|
|
|
790 $cmd_line .= "samtools view -bS $$files_ref->{sam_dedup_file_1_full} > $$files_ref->{bam_dedup_file_1_full}\n";
|
|
|
791 $cmd_line .= "samtools sort -n $$files_ref->{bam_dedup_file_1_full} $$files_ref->{bam_dedup_file_1_full_prefix}\n";
|
|
|
792 $cmd_line .= "samtools view -h $$files_ref->{bam_dedup_file_1_full_sorted} > $$files_ref->{sam_dedup_file_1_full_sorted}\n";
|
|
|
793
|
|
|
794 if ( $$reads_ref eq 'paired' ) { # Need to make this possible to be reverse only too
|
|
|
795
|
|
|
796 $cmd_line .= "sort -k1,1 $$files_ref->{sam_on_target_file_1} > $$files_ref->{sam_on_target_file_1_linux_sorted}\n";
|
|
|
797 $cmd_line .= "sort -k1,1 $$files_ref->{sam_off_target_file_1} > $$files_ref->{sam_off_target_file_1_linux_sorted}\n";
|
|
|
798 $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_on_target_file_1} > $$files_ref->{sam_dedup_on_target_file_1_linux_sorted}\n";
|
|
|
799 $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_off_target_file_1} > $$files_ref->{sam_dedup_off_target_file_1_linux_sorted}\n";
|
|
|
800 $cmd_line .= "sort -k1,1 $$files_ref->{sam_on_target_alone_file_2} > $$files_ref->{sam_on_target_alone_file_2_linux_sorted}\n";
|
|
|
801 $cmd_line .= "sort -k1,1 $$files_ref->{sam_off_target_alone_file_2} > $$files_ref->{sam_off_target_alone_file_2_linux_sorted}\n";
|
|
|
802 $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_on_target_alone_file_2} > $$files_ref->{sam_dedup_on_target_alone_file_2_linux_sorted}\n";
|
|
|
803 $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_off_target_alone_file_2} > $$files_ref->{sam_dedup_off_target_alone_file_2_linux_sorted}\n";
|
|
|
804 $cmd_line .= "sort -k1,1 $$files_ref->{sam_on_target_file_2} > $$files_ref->{sam_on_target_file_2_linux_sorted}\n";
|
|
|
805 $cmd_line .= "sort -k1,1 $$files_ref->{sam_off_target_file_2} > $$files_ref->{sam_off_target_file_2_linux_sorted}\n";
|
|
|
806 $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_on_target_file_2} > $$files_ref->{sam_dedup_on_target_file_2_linux_sorted}\n";
|
|
|
807 $cmd_line .= "sort -k1,1 $$files_ref->{sam_dedup_off_target_file_2} > $$files_ref->{sam_dedup_off_target_file_2_linux_sorted}\n";
|
|
|
808
|
|
|
809 $cmd_line .= "samtools view -bS $$files_ref->{sam_file_2_full} > $$files_ref->{bam_file_2_full}\n";
|
|
|
810 $cmd_line .= "samtools sort -n $$files_ref->{bam_file_2_full} $$files_ref->{bam_file_2_full_prefix}\n";
|
|
|
811 $cmd_line .= "samtools view -h $$files_ref->{bam_file_2_full_sorted} > $$files_ref->{sam_file_2_full_sorted}\n";
|
|
|
812 $cmd_line .= "samtools view -bS $$files_ref->{sam_dedup_file_2_full} > $$files_ref->{bam_dedup_file_2_full}\n";
|
|
|
813 $cmd_line .= "samtools sort -n $$files_ref->{bam_dedup_file_2_full} $$files_ref->{bam_dedup_file_2_full_prefix}\n";
|
|
|
814 $cmd_line .= "samtools view -h $$files_ref->{bam_dedup_file_2_full_sorted} > $$files_ref->{sam_dedup_file_2_full_sorted}\n";
|
|
|
815 }
|
|
|
816 return $cmd_line;
|
|
|
817 }
|
|
|
818
|
|
|
819
|
|
|
820 sub on_target_stats {
|
|
|
821 my $reads_ref = shift;
|
|
|
822 my $parameters_ref = shift;
|
|
|
823 my $files_ref = shift;
|
|
|
824 my $cmd_line = "echo On-target Stats\n";
|
|
|
825
|
|
|
826 if ( -e $$files_ref->{target_regions_file} ) {
|
|
|
827 if ( -s $$files_ref->{target_regions_file} ) {
|
|
|
828
|
|
|
829 if ( $$reads_ref eq 'single' ) { # Need to make this possible to be reverse only too
|
|
|
830
|
|
|
831 # Counts of on- and off-target reads
|
|
|
832 $cmd_line .= "$$parameters_ref->{path}/on_target_counts.pl -on_alone_1 $$files_ref->{sam_on_target_alone_file_1_linux_sorted} -off_alone_1 $$files_ref->{sam_off_target_alone_file_1_linux_sorted} -o $$files_ref->{on_target_file}\n";
|
|
|
833 $cmd_line .= "$$parameters_ref->{path}/on_target_counts.pl -on_alone_1 $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted} -off_alone_1 $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted} -o $$files_ref->{on_target_dedup_file}\n";
|
|
|
834
|
|
|
835 # On-target Stats and Housekeeping Stats
|
|
|
836 $cmd_line .= "$$parameters_ref->{path}/on_target_stats.pl -t $$files_ref->{target_regions_file} -i1 $$files_ref->{intersect_file_1} -o $$files_ref->{reads_per_exon_file} -oh $$files_ref->{housekeeping_file}\n";
|
|
|
837 $cmd_line .= "$$parameters_ref->{path}/on_target_stats.pl -t $$files_ref->{target_regions_file} -i1 $$files_ref->{intersect_dedup_file_1} -o $$files_ref->{reads_per_exon_dedup_file} -oh $$files_ref->{housekeeping_dedup_file} -om $$files_ref->{reads_per_exon_dedup_file_machine}\n";
|
|
|
838 }
|
|
|
839 else{
|
|
|
840 # Counts of on- and off-target reads
|
|
|
841 $cmd_line .= "$$parameters_ref->{path}/on_target_counts.pl -on_alone_1 $$files_ref->{sam_on_target_alone_file_1_linux_sorted} -on_alone_2 $$files_ref->{sam_on_target_alone_file_2_linux_sorted} -off_alone_1 $$files_ref->{sam_off_target_alone_file_1_linux_sorted} -off_alone_2 $$files_ref->{sam_off_target_alone_file_2_linux_sorted} -on_1 $$files_ref->{sam_on_target_file_1_linux_sorted} -on_2 $$files_ref->{sam_on_target_file_2_linux_sorted} -off_1 $$files_ref->{sam_off_target_file_1_linux_sorted} -off_2 $$files_ref->{sam_off_target_file_2_linux_sorted} -o $$files_ref->{on_target_file}\n";
|
|
|
842 $cmd_line .= "$$parameters_ref->{path}/on_target_counts.pl -on_alone_1 $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted} -on_alone_2 $$files_ref->{sam_dedup_on_target_alone_file_2_linux_sorted} -off_alone_1 $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted} -off_alone_2 $$files_ref->{sam_dedup_off_target_alone_file_2_linux_sorted} -on_1 $$files_ref->{sam_dedup_on_target_file_1_linux_sorted} -on_2 $$files_ref->{sam_dedup_on_target_file_2_linux_sorted} -off_1 $$files_ref->{sam_dedup_off_target_file_1_linux_sorted} -off_2 $$files_ref->{sam_dedup_off_target_file_2_linux_sorted} -o $$files_ref->{on_target_dedup_file}\n";
|
|
|
843
|
|
|
844 # On-target Stats and Housekeeping Stats
|
|
|
845 $cmd_line .= "$$parameters_ref->{path}/on_target_stats.pl -t $$files_ref->{target_regions_file} -i1 $$files_ref->{intersect_file_1} -i2 $$files_ref->{intersect_file_2} -o $$files_ref->{reads_per_exon_file} -oh $$files_ref->{housekeeping_file}\n";
|
|
|
846
|
|
|
847 $cmd_line .= "$$parameters_ref->{path}/on_target_stats.pl -t $$files_ref->{target_regions_file} -i1 $$files_ref->{intersect_dedup_file_1} -i2 $$files_ref->{intersect_dedup_file_2} -o $$files_ref->{reads_per_exon_dedup_file} -oh $$files_ref->{housekeeping_dedup_file} -om $$files_ref->{reads_per_exon_dedup_file_machine}\n";
|
|
|
848 }
|
|
|
849 }
|
|
|
850 }
|
|
|
851 return $cmd_line;
|
|
|
852 }
|
|
|
853
|
|
|
854 sub total_molecule_counts {
|
|
|
855 my $reads_ref = shift;
|
|
|
856 my $parameters_ref = shift;
|
|
|
857 my $files_ref = shift;
|
|
|
858 my $cmd_line = "echo Total Molecule Counts\n";
|
|
|
859 if ( $$reads_ref eq 'single' ) {
|
|
|
860 $cmd_line .= "python $$parameters_ref->{path}/count_reads_and_alignments_v2.py -r1 $$files_ref->{sam_file_1_full_sorted} -o $$files_ref->{total_and_aligned_molecule_count_per_tag_file}\n";
|
|
|
861 }
|
|
|
862 else {
|
|
|
863 $cmd_line .= "python $$parameters_ref->{path}/count_reads_and_alignments_v2.py -r1 $$files_ref->{sam_file_1_full_sorted} -r2 $$files_ref->{sam_file_2_full_sorted} -o $$files_ref->{total_and_aligned_molecule_count_per_tag_file}\n";
|
|
|
864 }
|
|
|
865 return $cmd_line;
|
|
|
866 }
|
|
|
867
|
|
|
868
|
|
|
869 sub de_duplicated_molecule_counts {
|
|
|
870 my $reads_ref = shift;
|
|
|
871 my $parameters_ref = shift;
|
|
|
872 my $files_ref = shift;
|
|
|
873 my $cmd_line = "echo De-duplicated Molecule Counts\n";
|
|
|
874 if ( $$reads_ref eq 'single' ) {
|
|
|
875 $cmd_line .= "python $$parameters_ref->{path}/count_reads_and_alignments_v2.py -r1 $$files_ref->{sam_dedup_file_1_full_sorted} -o $$files_ref->{unique_and_aligned_molecule_count_per_tag_file}\n";
|
|
|
876 }
|
|
|
877 else {
|
|
|
878 $cmd_line .= "python $$parameters_ref->{path}/count_reads_and_alignments_v2.py -r1 $$files_ref->{sam_dedup_file_1_full_sorted} -r2 $$files_ref->{sam_dedup_file_2_full_sorted} -o $$files_ref->{unique_and_aligned_molecule_count_per_tag_file}\n";
|
|
|
879 }
|
|
|
880 return $cmd_line;
|
|
|
881 }
|
|
|
882
|
|
|
883
|
|
|
884 sub all_molecule_counts {
|
|
|
885 my $parameters_ref = shift;
|
|
|
886 my $files_ref = shift;
|
|
|
887 my $cmd_line = "echo All Molecule Counts\n";
|
|
|
888 $cmd_line .= "$$parameters_ref->{path}/counts_2.pl -tamc $$files_ref->{total_and_aligned_molecule_count_per_tag_file} -uamc $$files_ref->{unique_and_aligned_molecule_count_per_tag_file} -otd $$files_ref->{on_target_dedup_file} -ot $$files_ref->{on_target_file} -o $$files_ref->{counts_file} -om $$files_ref->{counts_file_machine}\n";
|
|
|
889 return $cmd_line;
|
|
|
890 }
|
|
|
891
|
|
|
892 sub qc_check {
|
|
|
893 my $parameters_ref = shift;
|
|
|
894 my $files_ref = shift;
|
|
|
895 my $cmd_line = "echo QC Check\n";
|
|
|
896 $cmd_line .= "$$parameters_ref->{path}/qc_check.pl -hd $$files_ref->{housekeeping_dedup_file} -o $$files_ref->{qc_filter_file} -om $$files_ref->{qc_filter_file_machine}\n";
|
|
|
897 return $cmd_line;
|
|
|
898 }
|
|
|
899
|
|
|
900 sub coverage_uniformity {
|
|
|
901 my $reads_ref = shift;
|
|
|
902 my $parameters_ref = shift;
|
|
|
903 my $files_ref = shift;
|
|
|
904 my $cmd_line = "echo Coverage Uniformity\n";
|
|
|
905 $cmd_line .= "$$parameters_ref->{path}/coverage_uniformity.pl -hd $$files_ref->{housekeeping_dedup_file} -r $$reads_ref -o $$files_ref->{coverage_uniformity_file} -om $$files_ref->{coverage_uniformity_file_machine}\n";
|
|
|
906 return $cmd_line;
|
|
|
907 }
|
|
|
908
|
|
|
909
|
|
|
910 sub summary {
|
|
|
911 my $tag_ref = shift;
|
|
|
912 my $parameters_ref = shift;
|
|
|
913 my $files_ref = shift;
|
|
|
914 my $cmd_line = "echo Summary\n";
|
|
|
915
|
|
|
916 # my $sample_name = "'" . @$samples_array_ref[$sample_element_number] . "'";
|
|
|
917
|
|
|
918 $cmd_line .= "$$parameters_ref->{path}/summary.pl -s $$tag_ref -o $$files_ref->{summary_file} -om $$files_ref->{summary_file_machine}\n";
|
|
|
919 $cmd_line .= "cat $$files_ref->{qc_filter_file} >> $$files_ref->{summary_file}\n";
|
|
|
920 # $cmd_line .= "cat $$files_ref->{coverage_uniformity_file} >> $$files_ref->{summary_file}\n";
|
|
|
921 $cmd_line .= "cat $$files_ref->{counts_file} >> $$files_ref->{summary_file}\n";
|
|
|
922 if ( -e $$files_ref->{reads_per_exon_dedup_file} ) {
|
|
|
923 if ( -s $$files_ref->{reads_per_exon_dedup_file} ) {
|
|
|
924 $cmd_line .= "cat $$files_ref->{reads_per_exon_dedup_file} >> $$files_ref->{summary_file}\n";
|
|
|
925 }
|
|
|
926 }
|
|
|
927 $cmd_line .= "cat $$files_ref->{fusion_counts_with_splice_bare_file} >> $$files_ref->{summary_file}\n";
|
|
|
928 # $cmd_line .= "enscript -f Courier8 -p $$files_ref->{summary_file_ps} $$files_ref->{summary_file}\n";
|
|
|
929 # $cmd_line .= "ps2pdf $$files_ref->{summary_file_ps} $$files_ref->{summary_file_pdf}\n";
|
|
|
930
|
|
|
931 # Machine Readable Summary File
|
|
|
932 $cmd_line .= "cat $$files_ref->{qc_filter_file_machine} >> $$files_ref->{summary_file_machine}\n";
|
|
|
933 # $cmd_line .= "cat $$files_ref->{coverage_uniformity_file_machine} >> $$files_ref->{summary_file_machine}\n";
|
|
|
934 $cmd_line .= "cat $$files_ref->{counts_file_machine} >> $$files_ref->{summary_file_machine}\n";
|
|
|
935 if ( -e $$files_ref->{reads_per_exon_dedup_file_machine} ) {
|
|
|
936 if ( -s $$files_ref->{reads_per_exon_dedup_file_machine} ) {
|
|
|
937 $cmd_line .= "cat $$files_ref->{reads_per_exon_dedup_file_machine} >> $$files_ref->{summary_file_machine}\n";
|
|
|
938 }
|
|
|
939 }
|
|
|
940 $cmd_line .= "cat $$files_ref->{fusion_counts_with_splice_bare_file_machine} >> $$files_ref->{summary_file_machine}\n";
|
|
|
941
|
|
|
942 return $cmd_line;
|
|
|
943 }
|
|
|
944
|
|
|
945
|
|
|
946 sub clean_up {
|
|
|
947 my $reads_ref = shift;
|
|
|
948 my $parameters_ref = shift;
|
|
|
949 my $files_ref = shift;
|
|
|
950 my $file;
|
|
|
951 my $cmd_line = "echo Clean Up\n";
|
|
|
952
|
|
|
953 # Clean up Flanking Sequences Files
|
|
|
954 $cmd_line .= "$$parameters_ref->{path}/clean_up_flanking_sequences.pl -f $$files_ref->{flanking_sequences_file}\n";
|
|
|
955
|
|
|
956 # Clean up Flanking Splice Sequences Files
|
|
|
957 $cmd_line .= "$$parameters_ref->{path}/clean_up_flanking_sequences.pl -f $$files_ref->{flanking_splice_sequences_file}\n";
|
|
|
958
|
|
|
959 # Clean up
|
|
|
960 $cmd_line .= "rm $$files_ref->{sam_file_1_full}\n";
|
|
|
961 $cmd_line .= "rm $$files_ref->{bam_file_1}\n";
|
|
|
962 $cmd_line .= "rm $$files_ref->{bed_file_1}\n";
|
|
|
963 $cmd_line .= "rm $$files_ref->{bed_file_combined}\n";
|
|
|
964 $cmd_line .= "rm $$files_ref->{sam_dedup_file_1}\n";
|
|
|
965 $cmd_line .= "rm $$files_ref->{sam_dedup_file_1_full}\n";
|
|
|
966 $cmd_line .= "rm $$files_ref->{bam_dedup_file_1}\n";
|
|
|
967 $cmd_line .= "rm $$files_ref->{full_master_prejoin_file_1}\n";
|
|
|
968 $cmd_line .= "rm $$files_ref->{full_master_file_1}\n";
|
|
|
969 $cmd_line .= "rm $$files_ref->{full_master_dedup_prejoin_file_1}\n";
|
|
|
970 $cmd_line .= "rm $$files_ref->{full_master_dedup_file_1}\n";
|
|
|
971 $cmd_line .= "rm $$files_ref->{bed_points_file_1}\n";
|
|
|
972 $cmd_line .= "rm $$files_ref->{bed_points_dedup_file_1}\n";
|
|
|
973 $cmd_line .= "rm $$files_ref->{intersect_file_1}\n";
|
|
|
974 $cmd_line .= "rm $$files_ref->{intersect_dedup_file_1}\n";
|
|
|
975 $cmd_line .= "rm $$files_ref->{sam_on_target_alone_file_1}\n";
|
|
|
976 $cmd_line .= "rm $$files_ref->{sam_off_target_alone_file_1}\n";
|
|
|
977 $cmd_line .= "rm $$files_ref->{master_dedup_no_annotation_file_1}\n";
|
|
|
978 $cmd_line .= "rm $$files_ref->{master_dedup_prejoin_file_1}\n";
|
|
|
979 $cmd_line .= "rm $$files_ref->{master_dedup_file_1}\n";
|
|
|
980 $cmd_line .= "rm $$files_ref->{fusion_reads_file}\n";
|
|
|
981 $cmd_line .= "rm $$files_ref->{fusion_counts_file}\n";
|
|
|
982 $cmd_line .= "rm $$files_ref->{fusion_counts_bare_file}\n";
|
|
|
983 # $file = $$files_ref->{flanking_sequences_file} . ".tmp~";
|
|
|
984 # $cmd_line .= "rm $file\n";
|
|
|
985 # $file = $$files_ref->{flanking_splice_sequences_file} . ".tmp~";
|
|
|
986 # $cmd_line .= "rm $file\n";
|
|
|
987 $cmd_line .= "rm $$files_ref->{splice_counts_file}\n";
|
|
|
988 $cmd_line .= "rm $$files_ref->{splice_counts_bare_file}\n";
|
|
|
989 $cmd_line .= "rm $$files_ref->{fusion_counts_with_splice_bare_file}\n";
|
|
|
990 $cmd_line .= "rm $$files_ref->{fusion_counts_with_splice_bare_file_machine}\n";
|
|
|
991 $cmd_line .= "rm $$files_ref->{splice_reads_file}\n";
|
|
|
992 $cmd_line .= "rm $$files_ref->{sam_on_target_alone_file_1_linux_sorted}\n";
|
|
|
993 $cmd_line .= "rm $$files_ref->{sam_off_target_alone_file_1_linux_sorted}\n";
|
|
|
994 $cmd_line .= "rm $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted}\n";
|
|
|
995 $cmd_line .= "rm $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted}\n";
|
|
|
996 $cmd_line .= "rm $$files_ref->{housekeeping_dedup_file}\n";
|
|
|
997 $cmd_line .= "rm $$files_ref->{on_target_dedup_file}\n";
|
|
|
998 $cmd_line .= "rm $$files_ref->{reads_per_exon_dedup_file}\n";
|
|
|
999 $cmd_line .= "rm $$files_ref->{reads_per_exon_dedup_file_machine}\n";
|
|
|
1000 $cmd_line .= "rm $$files_ref->{housekeeping_file}\n";
|
|
|
1001 $cmd_line .= "rm $$files_ref->{on_target_file}\n";
|
|
|
1002 $cmd_line .= "rm $$files_ref->{reads_per_exon_file}\n";
|
|
|
1003 $cmd_line .= "rm $$files_ref->{sam_file_1_marked}\n";
|
|
|
1004 $cmd_line .= "rm $$files_ref->{sam_dedup_file_1_marked}\n";
|
|
|
1005 $cmd_line .= "rm $$files_ref->{bam_file_1_full}\n";
|
|
|
1006 $cmd_line .= "rm $$files_ref->{bam_file_1_full_sorted}\n";
|
|
|
1007 $cmd_line .= "rm $$files_ref->{sam_file_1_full_sorted}\n";
|
|
|
1008 # $cmd_line .= "rm $$files_ref->{total_and_aligned_molecule_count_file_1}\n";
|
|
|
1009 $cmd_line .= "rm $$files_ref->{total_and_aligned_molecule_count_per_tag_file}\n";
|
|
|
1010 # $cmd_line .= "rm $$files_ref->{unique_and_aligned_molecule_count_file_1}\n";
|
|
|
1011 $cmd_line .= "rm $$files_ref->{unique_and_aligned_molecule_count_per_tag_file}\n";
|
|
|
1012 $cmd_line .= "rm $$files_ref->{bam_dedup_file_1_full}\n";
|
|
|
1013 $cmd_line .= "rm $$files_ref->{bam_dedup_file_1_full_sorted}\n";
|
|
|
1014 $cmd_line .= "rm $$files_ref->{sam_dedup_file_1_full_sorted}\n";
|
|
|
1015 $cmd_line .= "rm $$files_ref->{qc_filter_file}\n";
|
|
|
1016 $cmd_line .= "rm $$files_ref->{qc_filter_file_machine}\n";
|
|
|
1017 $cmd_line .= "rm $$files_ref->{coverage_uniformity_file}\n";
|
|
|
1018 $cmd_line .= "rm $$files_ref->{coverage_uniformity_file_machine}\n";
|
|
|
1019 $cmd_line .= "rm $$files_ref->{counts_file}\n";
|
|
|
1020 $cmd_line .= "rm $$files_ref->{counts_file_machine}\n";
|
|
|
1021 # $cmd_line .= "rm $$files_ref->{summary_file_ps}\n";
|
|
|
1022 if ( $$reads_ref eq 'paired' ) {
|
|
|
1023 $cmd_line .= "rm $$files_ref->{sam_file_2_full}\n";
|
|
|
1024 $cmd_line .= "rm $$files_ref->{bam_file_2}\n";
|
|
|
1025 $cmd_line .= "rm $$files_ref->{bed_file_2}\n";
|
|
|
1026 $cmd_line .= "rm $$files_ref->{sam_dedup_file_2}\n";
|
|
|
1027 $cmd_line .= "rm $$files_ref->{sam_dedup_file_2_full}\n";
|
|
|
1028 $cmd_line .= "rm $$files_ref->{bam_dedup_file_2}\n";
|
|
|
1029 $cmd_line .= "rm $$files_ref->{full_master_prejoin_file_2}\n";
|
|
|
1030 $cmd_line .= "rm $$files_ref->{full_master_file_2}\n";
|
|
|
1031 $cmd_line .= "rm $$files_ref->{full_master_dedup_prejoin_file_2}\n";
|
|
|
1032 $cmd_line .= "rm $$files_ref->{full_master_dedup_file_2}\n";
|
|
|
1033 $cmd_line .= "rm $$files_ref->{bed_points_file_2}\n";
|
|
|
1034 $cmd_line .= "rm $$files_ref->{bed_points_dedup_file_2}\n";
|
|
|
1035 $cmd_line .= "rm $$files_ref->{intersect_file_2}\n";
|
|
|
1036 $cmd_line .= "rm $$files_ref->{intersect_dedup_file_2}\n";
|
|
|
1037 $cmd_line .= "rm $$files_ref->{intersect_file_combined}\n";
|
|
|
1038 $cmd_line .= "rm $$files_ref->{intersect_dedup_file_combined}\n";
|
|
|
1039 $cmd_line .= "rm $$files_ref->{sam_dedup_on_target_alone_file_1}\n";
|
|
|
1040 $cmd_line .= "rm $$files_ref->{sam_dedup_off_target_alone_file_1}\n";
|
|
|
1041 $cmd_line .= "rm $$files_ref->{sam_on_target_file_1}\n";
|
|
|
1042 $cmd_line .= "rm $$files_ref->{sam_off_target_file_1}\n";
|
|
|
1043 $cmd_line .= "rm $$files_ref->{sam_on_target_file_2}\n";
|
|
|
1044 $cmd_line .= "rm $$files_ref->{sam_off_target_file_2}\n";
|
|
|
1045 $cmd_line .= "rm $$files_ref->{sam_on_target_alone_file_2}\n";
|
|
|
1046 $cmd_line .= "rm $$files_ref->{sam_off_target_alone_file_2}\n";
|
|
|
1047 $cmd_line .= "rm $$files_ref->{sam_dedup_on_target_alone_file_2}\n";
|
|
|
1048 $cmd_line .= "rm $$files_ref->{sam_dedup_off_target_alone_file_2}\n";
|
|
|
1049 $cmd_line .= "rm $$files_ref->{master_dedup_no_annotation_file_2}\n";
|
|
|
1050 $cmd_line .= "rm $$files_ref->{master_dedup_prejoin_file_2}\n";
|
|
|
1051 $cmd_line .= "rm $$files_ref->{master_dedup_file_2}\n";
|
|
|
1052 $cmd_line .= "rm $$files_ref->{sam_on_target_file_1_linux_sorted}\n";
|
|
|
1053 $cmd_line .= "rm $$files_ref->{sam_off_target_file_1_linux_sorted}\n";
|
|
|
1054 $cmd_line .= "rm $$files_ref->{sam_dedup_on_target_file_1_linux_sorted}\n";
|
|
|
1055 $cmd_line .= "rm $$files_ref->{sam_dedup_off_target_file_1_linux_sorted}\n";
|
|
|
1056 $cmd_line .= "rm $$files_ref->{sam_on_target_alone_file_2_linux_sorted}\n";
|
|
|
1057 $cmd_line .= "rm $$files_ref->{sam_off_target_alone_file_2_linux_sorted}\n";
|
|
|
1058 $cmd_line .= "rm $$files_ref->{sam_dedup_on_target_alone_file_2_linux_sorted}\n";
|
|
|
1059 $cmd_line .= "rm $$files_ref->{sam_dedup_off_target_alone_file_2_linux_sorted}\n";
|
|
|
1060 $cmd_line .= "rm $$files_ref->{sam_on_target_file_2_linux_sorted}\n";
|
|
|
1061 $cmd_line .= "rm $$files_ref->{sam_off_target_file_2_linux_sorted}\n";
|
|
|
1062 $cmd_line .= "rm $$files_ref->{sam_dedup_on_target_file_2_linux_sorted}\n";
|
|
|
1063 $cmd_line .= "rm $$files_ref->{sam_dedup_off_target_file_2_linux_sorted}\n";
|
|
|
1064 $cmd_line .= "rm $$files_ref->{sam_file_2_marked}\n";
|
|
|
1065 $cmd_line .= "rm $$files_ref->{sam_dedup_file_2_marked}\n";
|
|
|
1066 $cmd_line .= "rm $$files_ref->{bam_file_2_full}\n";
|
|
|
1067 $cmd_line .= "rm $$files_ref->{bam_file_2_full_sorted}\n";
|
|
|
1068 $cmd_line .= "rm $$files_ref->{sam_file_2_full_sorted}\n";
|
|
|
1069 # $cmd_line .= "rm $$files_ref->{total_and_aligned_molecule_count_file_2}\n";
|
|
|
1070 # $cmd_line .= "rm $$files_ref->{unique_and_aligned_molecule_count_file_2}\n";
|
|
|
1071 $cmd_line .= "rm $$files_ref->{bam_dedup_file_2_full}\n";
|
|
|
1072 $cmd_line .= "rm $$files_ref->{bam_dedup_file_2_full_sorted}\n";
|
|
|
1073 $cmd_line .= "rm $$files_ref->{sam_dedup_file_2_full_sorted}\n";
|
|
|
1074 }
|
|
|
1075
|
|
|
1076 return $cmd_line;
|
|
|
1077 }
|
|
|
1078
|
|
|
1079
|
|
|
1080 sub summary_for_unprocessed_sample {
|
|
|
1081 my $reads_ref = shift;
|
|
|
1082 my $fastq_file_1_ref = shift;
|
|
|
1083 my $fastq_file_2_ref = shift;
|
|
|
1084 my $parameters_ref = shift;
|
|
|
1085 my $files_ref = shift;
|
|
|
1086 my $cmd_line = "echo Summary for Unprocessed Sample\n";
|
|
|
1087 $cmd_line .= "$$parameters_ref->{path}/summary_for_unprocessed_samples.pl -r $$reads_ref -f1 $$fastq_file_1_ref -f2 $$fastq_file_2_ref -o $$files_ref->{summary_file} -om $$files_ref->{summary_file_machine}\n";
|
|
|
1088 # $cmd_line .= "enscript -f Courier8 -p $$files_ref->{summary_file_ps} $$files_ref->{summary_file}\n";
|
|
|
1089 # $cmd_line .= "ps2pdf $$files_ref->{summary_file_ps} $$files_ref->{summary_file_pdf}\n";
|
|
|
1090 return $cmd_line;
|
|
|
1091 }
|
|
|
1092
|
|
|
1093
|
|
|
1094 sub join_multiple_samples {
|
|
|
1095 my $parameters_ref = shift;
|
|
|
1096 my $cmd_line = "echo Join Multiple Samples\n";
|
|
|
1097 $cmd_line = "$$parameters_ref->{path}/join_multisample_output.pl -config $$parameters_ref->{config_file} -o $$parameters_ref->{outputfile}\n";
|
|
|
1098 return $cmd_line;
|
|
|
1099 }
|
|
|
1100
|
|
|
1101 #sub define_alignment_file_names {
|
|
|
1102 # my $reads_ref = shift;
|
|
|
1103 # my $tags_array_ref = shift;
|
|
|
1104 # my $parameters_ref = shift;
|
|
|
1105 # my $files_ref = shift;
|
|
|
1106 # $$files_ref->{sam_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam";
|
|
|
1107 # $$files_ref->{sam_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.full";
|
|
|
1108 # if ( $$reads_ref eq 'paired' ) {
|
|
|
1109 # $$files_ref->{sam_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam";
|
|
|
1110 # $$files_ref->{sam_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.full";
|
|
|
1111 # }
|
|
|
1112 #}
|
|
|
1113
|
|
|
1114 sub define_alignments_file_names {
|
|
|
1115 my $reads_ref = shift;
|
|
|
1116 my $tags_array_ref = shift;
|
|
|
1117 my $tag_ref = shift;
|
|
|
1118 my $parameters_ref = shift;
|
|
|
1119 my $files_ref = shift;
|
|
|
1120 $$files_ref->{sam_file_1_orig} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".fastq.sam";
|
|
|
1121 $$files_ref->{sam_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.full";
|
|
|
1122 $$files_ref->{sam_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam";
|
|
|
1123 $$files_ref->{bam_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bam";
|
|
|
1124 $$files_ref->{bed_file_1_orig} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bed.orig";
|
|
|
1125 if ( $$reads_ref eq 'paired' ) {
|
|
|
1126 $$files_ref->{sam_file_2_orig} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".fastq.sam";
|
|
|
1127 $$files_ref->{sam_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.full";
|
|
|
1128 $$files_ref->{sam_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam";
|
|
|
1129 $$files_ref->{bam_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bam";
|
|
|
1130 $$files_ref->{bed_file_2_orig} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bed.orig";
|
|
|
1131 }
|
|
|
1132 $$files_ref->{bed_file_combined} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".combined.bed";
|
|
|
1133 }
|
|
|
1134
|
|
|
1135 sub define_de_duplication_file_names {
|
|
|
1136 my $reads_ref = shift;
|
|
|
1137 my $tags_array_ref = shift;
|
|
|
1138 my $tag_ref = shift;
|
|
|
1139 my $parameters_ref = shift;
|
|
|
1140 my $files_ref = shift;
|
|
|
1141 $$files_ref->{dedup_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup_read_ids.dat";
|
|
|
1142 $$files_ref->{sam_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.dedup";
|
|
|
1143 $$files_ref->{sam_dedup_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.sam.full";
|
|
|
1144 if ( $$reads_ref eq 'paired' ) {
|
|
|
1145 $$files_ref->{sam_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.dedup";
|
|
|
1146 $$files_ref->{sam_dedup_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.sam.full";
|
|
|
1147 }
|
|
|
1148 }
|
|
|
1149
|
|
|
1150 sub define_on_and_off_target_file_names {
|
|
|
1151 my $reads_ref = shift;
|
|
|
1152 my $tags_array_ref = shift;
|
|
|
1153 my $tag_ref = shift;
|
|
|
1154 my $parameters_ref = shift;
|
|
|
1155 my $files_ref = shift;
|
|
|
1156 # File 1
|
|
|
1157 $$files_ref->{target_regions_bed_file} = $$parameters_ref->{directory} . "/target_regions.bed";
|
|
|
1158 $$files_ref->{full_master_prejoin_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".full.prejoin.master.dat";
|
|
|
1159 $$files_ref->{full_master_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".full.master.dat";
|
|
|
1160 $$files_ref->{bed_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bed";
|
|
|
1161 $$files_ref->{bed_points_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".points.bed";
|
|
|
1162 $$files_ref->{intersect_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".intersect.dat";
|
|
|
1163 $$files_ref->{sam_on_target_alone_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".on_target.alone.sam";
|
|
|
1164 $$files_ref->{sam_file_1_marked} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.marked";
|
|
|
1165 $$files_ref->{sam_off_target_alone_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".off_target.alone.sam";
|
|
|
1166 $$files_ref->{sam_on_target_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".on_target.sam";
|
|
|
1167 $$files_ref->{sam_off_target_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".off_target.sam";
|
|
|
1168 # File 1 Dedup
|
|
|
1169 $$files_ref->{full_master_dedup_prejoin_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".full.dedup.prejoin.master.dat";
|
|
|
1170 $$files_ref->{full_master_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".full.dedup.master.dat";
|
|
|
1171 $$files_ref->{bed_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.bed";
|
|
|
1172 $$files_ref->{bed_points_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.points.bed";
|
|
|
1173 $$files_ref->{intersect_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.intersect.dat";
|
|
|
1174 $$files_ref->{sam_dedup_on_target_alone_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.on_target.alone.sam";
|
|
|
1175 $$files_ref->{sam_dedup_file_1_marked} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.dedup.marked";
|
|
|
1176 $$files_ref->{sam_dedup_off_target_alone_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.off_target.alone.sam";
|
|
|
1177 $$files_ref->{sam_dedup_on_target_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.on_target.sam";
|
|
|
1178 $$files_ref->{sam_dedup_off_target_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.off_target.sam";
|
|
|
1179 # File 2
|
|
|
1180 if ( $$reads_ref eq 'paired' ) {
|
|
|
1181 $$files_ref->{full_master_prejoin_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".full.prejoin.master.dat";
|
|
|
1182 $$files_ref->{full_master_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".full.master.dat";
|
|
|
1183 $$files_ref->{bed_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bed";
|
|
|
1184 $$files_ref->{bed_points_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".points.bed";
|
|
|
1185 $$files_ref->{intersect_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".intersect.dat";
|
|
|
1186 $$files_ref->{sam_on_target_alone_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".on_target.alone.sam";
|
|
|
1187 $$files_ref->{sam_file_2_marked} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.marked";
|
|
|
1188 $$files_ref->{sam_off_target_alone_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".off_target.alone.sam";
|
|
|
1189 $$files_ref->{sam_on_target_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".on_target.sam";
|
|
|
1190 $$files_ref->{sam_off_target_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".off_target.sam";
|
|
|
1191 }
|
|
|
1192 # File 2 Dedup
|
|
|
1193 if ( $$reads_ref eq 'paired' ) {
|
|
|
1194 $$files_ref->{full_master_dedup_prejoin_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".full.dedup.prejoin.master.dat";
|
|
|
1195 $$files_ref->{full_master_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".full.dedup.master.dat";
|
|
|
1196 $$files_ref->{bed_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.bed";
|
|
|
1197 $$files_ref->{bed_points_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.points.bed";
|
|
|
1198 $$files_ref->{intersect_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.intersect.dat";
|
|
|
1199 $$files_ref->{sam_dedup_on_target_alone_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.on_target.alone.sam";
|
|
|
1200 $$files_ref->{sam_dedup_file_2_marked} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.dedup.marked";
|
|
|
1201 $$files_ref->{sam_dedup_off_target_alone_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.off_target.alone.sam";
|
|
|
1202 $$files_ref->{sam_dedup_on_target_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.on_target.sam";
|
|
|
1203 $$files_ref->{sam_dedup_off_target_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.off_target.sam";
|
|
|
1204 }
|
|
|
1205 $$files_ref->{intersect_file_combined} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".intersect_combined.dat";
|
|
|
1206 $$files_ref->{intersect_dedup_file_combined} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup.intersect_combined.dat";
|
|
|
1207 }
|
|
|
1208
|
|
|
1209 sub define_coverage_and_start_site_file_names {
|
|
|
1210 my $reads_ref = shift;
|
|
|
1211 my $tags_array_ref = shift;
|
|
|
1212 my $parameters_ref = shift;
|
|
|
1213 my $files_ref = shift;
|
|
|
1214 $$files_ref->{start_site_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.start_site.bedgraph";
|
|
|
1215 $$files_ref->{coverage_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.coverage.bedgraph";
|
|
|
1216 if ( $$reads_ref eq 'paired' ) {
|
|
|
1217 $$files_ref->{start_site_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.start_site.bedgraph";
|
|
|
1218 $$files_ref->{coverage_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.coverage.bedgraph";
|
|
|
1219 }
|
|
|
1220 }
|
|
|
1221
|
|
|
1222 sub define_master_files_file_names {
|
|
|
1223 my $reads_ref = shift;
|
|
|
1224 my $tags_array_ref = shift;
|
|
|
1225 my $parameters_ref = shift;
|
|
|
1226 my $files_ref = shift;
|
|
|
1227 $$files_ref->{master_dedup_no_annotation_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.no_annotation.master.dat";
|
|
|
1228 $$files_ref->{master_dedup_prejoin_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.prejoin.master.dat";
|
|
|
1229 $$files_ref->{master_dedup_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.master.dat";
|
|
|
1230 if ( $$reads_ref eq 'paired' ) {
|
|
|
1231 $$files_ref->{master_dedup_no_annotation_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.no_annotation.master.dat";
|
|
|
1232 $$files_ref->{master_dedup_prejoin_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.prejoin.master.dat";
|
|
|
1233 $$files_ref->{master_dedup_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.master.dat";
|
|
|
1234 }
|
|
|
1235 }
|
|
|
1236
|
|
|
1237 sub define_fusion_reads_file_names {
|
|
|
1238 my $reads_ref = shift;
|
|
|
1239 my $tags_array_ref = shift;
|
|
|
1240 my $tag_ref = shift;
|
|
|
1241 my $parameters_ref = shift;
|
|
|
1242 my $files_ref = shift;
|
|
|
1243 $$files_ref->{one_segment_reads_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".one_segment_reads.dat";
|
|
|
1244 $$files_ref->{splice_reads_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".splice_reads.dat";
|
|
|
1245 $$files_ref->{fusion_reads_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".fusion_reads.dat";
|
|
|
1246 $$files_ref->{multi_fusion_reads_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".multi_fusion_reads.dat";
|
|
|
1247 if ( $$reads_ref eq 'paired' ) {
|
|
|
1248 $$files_ref->{one_segment_reads_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".one_segment_reads.dat";
|
|
|
1249 $$files_ref->{splice_reads_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".splice_reads.dat";
|
|
|
1250 $$files_ref->{fusion_reads_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".fusion_reads.dat";
|
|
|
1251 $$files_ref->{multi_fusion_reads_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".multi_fusion_reads.dat";
|
|
|
1252 }
|
|
|
1253 $$files_ref->{fusion_reads_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_reads.combined.dat";
|
|
|
1254 $$files_ref->{splice_reads_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".splice_reads.combined.dat";
|
|
|
1255 }
|
|
|
1256
|
|
|
1257 sub define_count_fusions_file_names {
|
|
|
1258 my $tag_ref = shift;
|
|
|
1259 my $parameters_ref = shift;
|
|
|
1260 my $files_ref = shift;
|
|
|
1261 $$files_ref->{fusion_counts_bare_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_counts_bare.dat";
|
|
|
1262 $$files_ref->{fusion_counts_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_counts.dat";
|
|
|
1263 $$files_ref->{splice_counts_bare_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".splice_counts_bare.dat";
|
|
|
1264 $$files_ref->{splice_counts_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".splice_counts.dat";
|
|
|
1265 $$files_ref->{fusion_counts_with_splice_bare_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_counts_with_splice_bare.dat";
|
|
|
1266 $$files_ref->{fusion_counts_with_splice_bare_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_counts_with_splice_bare.machine.dat";
|
|
|
1267 }
|
|
|
1268
|
|
|
1269 sub define_flanking_sequences_file_names {
|
|
|
1270 my $tag_ref = shift;
|
|
|
1271 my $parameters_ref = shift;
|
|
|
1272 my $files_ref = shift;
|
|
|
1273 $$files_ref->{flanking_sequences_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".flanking_sequences.dat";
|
|
|
1274 $$files_ref->{flanking_splice_sequences_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".flanking_splice_sequences.dat";
|
|
|
1275 }
|
|
|
1276
|
|
|
1277 sub define_consensus_sequences_file_names {
|
|
|
1278 my $tag_ref = shift;
|
|
|
1279 my $parameters_ref = shift;
|
|
|
1280 my $files_ref = shift;
|
|
|
1281 $$files_ref->{consensus_fusion_std_out_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".consensus_fusion_std_out.dat";
|
|
|
1282 $$files_ref->{consensus_fusion_std_err_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".consensus_fusion_std_err.dat";
|
|
|
1283 $$files_ref->{consensus_splice_std_out_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".consensus_splice_std_out.dat";
|
|
|
1284 $$files_ref->{consensus_splice_std_err_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".consensus_splice_std_err.dat";
|
|
|
1285 $$files_ref->{fusion_and_splice_consensus_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".fusion_and_splice_consensus_sequences.fasta";
|
|
|
1286 }
|
|
|
1287
|
|
|
1288 sub define_bam_dedup_files_file_names {
|
|
|
1289 my $reads_ref = shift;
|
|
|
1290 my $tags_array_ref = shift;
|
|
|
1291 my $parameters_ref = shift;
|
|
|
1292 my $files_ref = shift;
|
|
|
1293 $$files_ref->{bam_dedup_file_1} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[0] . ".dedup.bam";
|
|
|
1294 $$files_ref->{bam_dedup_sorted_file_1_name} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[0] . ".dedup.sorted";
|
|
|
1295 $$files_ref->{bam_dedup_sorted_file_1} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[0] . ".dedup.sorted.bam";
|
|
|
1296 if ( $$reads_ref eq 'paired' ) {
|
|
|
1297 $$files_ref->{bam_dedup_file_2} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[1] . ".dedup.bam";
|
|
|
1298 $$files_ref->{bam_dedup_sorted_file_2_name} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[1] . ".dedup.sorted";
|
|
|
1299 $$files_ref->{bam_dedup_sorted_file_2} = $$parameters_ref->{directory} . "/" . $$tags_array_ref[1] . ".dedup.sorted.bam";
|
|
|
1300 }
|
|
|
1301 }
|
|
|
1302
|
|
|
1303 sub define_sort_sam_files_file_names {
|
|
|
1304 my $reads_ref = shift;
|
|
|
1305 my $tags_array_ref = shift;
|
|
|
1306 my $parameters_ref = shift;
|
|
|
1307 my $files_ref = shift;
|
|
|
1308 $$files_ref->{sam_on_target_alone_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".on_target.alone.linux_sorted.sam";
|
|
|
1309 $$files_ref->{sam_off_target_alone_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".off_target.alone.linux_sorted.sam";
|
|
|
1310 $$files_ref->{sam_dedup_on_target_alone_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.on_target.alone.linux_sorted.sam";
|
|
|
1311 $$files_ref->{sam_dedup_off_target_alone_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.off_target.alone.linux_sorted.sam";
|
|
|
1312 $$files_ref->{sam_on_target_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".on_target.linux_sorted.sam";
|
|
|
1313 $$files_ref->{sam_off_target_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".off_target.linux_sorted.sam";
|
|
|
1314 $$files_ref->{sam_dedup_on_target_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.on_target.linux_sorted.sam";
|
|
|
1315 $$files_ref->{sam_dedup_off_target_file_1_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.off_target.linux_sorted.sam";
|
|
|
1316 if ( $$reads_ref eq 'paired' ) {
|
|
|
1317 $$files_ref->{sam_on_target_alone_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".on_target.alone.linux_sorted.sam";
|
|
|
1318 $$files_ref->{sam_off_target_alone_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".off_target.alone.linux_sorted.sam";
|
|
|
1319 $$files_ref->{sam_dedup_on_target_alone_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.on_target.alone.linux_sorted.sam";
|
|
|
1320 $$files_ref->{sam_dedup_off_target_alone_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.off_target.alone.linux_sorted.sam";
|
|
|
1321 $$files_ref->{sam_on_target_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".on_target.linux_sorted.sam";
|
|
|
1322 $$files_ref->{sam_off_target_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".off_target.linux_sorted.sam";
|
|
|
1323 $$files_ref->{sam_dedup_on_target_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.on_target.linux_sorted.sam";
|
|
|
1324 $$files_ref->{sam_dedup_off_target_file_2_linux_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.off_target.linux_sorted.sam";
|
|
|
1325 }
|
|
|
1326
|
|
|
1327 $$files_ref->{bam_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bam.full";
|
|
|
1328 $$files_ref->{bam_file_1_full_prefix} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".bam.full.prefix";
|
|
|
1329 $$files_ref->{bam_file_1_full_sorted} = $$files_ref->{bam_file_1_full_prefix} . ".bam";
|
|
|
1330 $$files_ref->{sam_file_1_full_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".sam.full.sorted";
|
|
|
1331 if ( $$reads_ref eq 'paired' ) {
|
|
|
1332 $$files_ref->{bam_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bam.full";
|
|
|
1333 $$files_ref->{bam_file_2_full_prefix} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".bam.full.prefix";
|
|
|
1334 $$files_ref->{bam_file_2_full_sorted} = $$files_ref->{bam_file_2_full_prefix} . ".bam";
|
|
|
1335 $$files_ref->{sam_file_2_full_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".sam.full.sorted";
|
|
|
1336 }
|
|
|
1337
|
|
|
1338 $$files_ref->{bam_dedup_file_1_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.bam.full";
|
|
|
1339 $$files_ref->{bam_dedup_file_1_full_prefix} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.bam.full.prefix";
|
|
|
1340 $$files_ref->{bam_dedup_file_1_full_sorted} = $$files_ref->{bam_dedup_file_1_full_prefix} . ".bam";
|
|
|
1341 $$files_ref->{sam_dedup_file_1_full_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".dedup.sam.full.sorted";
|
|
|
1342 if ( $$reads_ref eq 'paired' ) {
|
|
|
1343 $$files_ref->{bam_dedup_file_2_full} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.bam.full";
|
|
|
1344 $$files_ref->{bam_dedup_file_2_full_prefix} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.bam.full.prefix";
|
|
|
1345 $$files_ref->{bam_dedup_file_2_full_sorted} = $$files_ref->{bam_dedup_file_2_full_prefix} . ".bam";
|
|
|
1346 $$files_ref->{sam_dedup_file_2_full_sorted} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".dedup.sam.full.sorted";
|
|
|
1347 }
|
|
|
1348 }
|
|
|
1349
|
|
|
1350 sub define_on_target_stats_file_names {
|
|
|
1351 my $tag_ref = shift;
|
|
|
1352 my $parameters_ref = shift;
|
|
|
1353 my $files_ref = shift;
|
|
|
1354 $$files_ref->{on_target_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".on_target.dat";
|
|
|
1355 $$files_ref->{on_target_dedup_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup.on_target.dat";
|
|
|
1356 $$files_ref->{reads_per_exon_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".reads_per_exon.dat";
|
|
|
1357 $$files_ref->{housekeeping_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".housekeeping.dat";
|
|
|
1358 $$files_ref->{reads_per_exon_dedup_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup.reads_per_exon.dat";
|
|
|
1359 $$files_ref->{housekeeping_dedup_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".housekeeping.dedup.dat";
|
|
|
1360 $$files_ref->{reads_per_exon_dedup_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".dedup.reads_per_exon.machine.dat";
|
|
|
1361 }
|
|
|
1362
|
|
|
1363 sub define_total_molecule_counts_file_names {
|
|
|
1364 my $reads_ref = shift;
|
|
|
1365 my $tags_array_ref = shift;
|
|
|
1366 my $tag_ref = shift;
|
|
|
1367 my $parameters_ref = shift;
|
|
|
1368 my $files_ref = shift;
|
|
|
1369 $$files_ref->{total_and_aligned_molecule_count_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".total_and_aligned_molecule_count.dat";
|
|
|
1370 if ( $$reads_ref eq 'paired' ) {
|
|
|
1371 $$files_ref->{total_and_aligned_molecule_count_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".total_and_aligned_molecule_count.dat";
|
|
|
1372 }
|
|
|
1373 $$files_ref->{total_and_aligned_molecule_count_per_tag_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".per_tag.total_and_aligned_molecule_count.dat";
|
|
|
1374 }
|
|
|
1375
|
|
|
1376 sub define_de_deduplicated_molecule_counts_file_names {
|
|
|
1377 my $reads_ref = shift;
|
|
|
1378 my $tags_array_ref = shift;
|
|
|
1379 my $tag_ref = shift;
|
|
|
1380 my $parameters_ref = shift;
|
|
|
1381 my $files_ref = shift;
|
|
|
1382 $$files_ref->{unique_and_aligned_molecule_count_file_1} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[0] . ".unique_and_aligned_molecule_count.dat";
|
|
|
1383 if ( $$reads_ref eq 'paired' ) {
|
|
|
1384 $$files_ref->{unique_and_aligned_molecule_count_file_2} = $$parameters_ref->{directory} . "/" . @$tags_array_ref[1] . ".unique_and_aligned_molecule_count.dat";
|
|
|
1385 }
|
|
|
1386 $$files_ref->{unique_and_aligned_molecule_count_per_tag_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".per_tag.unique_and_aligned_molecule_count.dat";
|
|
|
1387 }
|
|
|
1388
|
|
|
1389 sub define_all_molecule_counts_file_names {
|
|
|
1390 my $tag_ref = shift;
|
|
|
1391 my $parameters_ref = shift;
|
|
|
1392 my $files_ref = shift;
|
|
|
1393 $$files_ref->{counts_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".counts.dat";
|
|
|
1394 $$files_ref->{counts_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".counts.machine.dat";
|
|
|
1395 }
|
|
|
1396
|
|
|
1397
|
|
|
1398 sub define_qc_check_file_names {
|
|
|
1399 my $tag_ref = shift;
|
|
|
1400 my $parameters_ref = shift;
|
|
|
1401 my $files_ref = shift;
|
|
|
1402 $$files_ref->{qc_filter_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".qc_filter.dat";
|
|
|
1403 $$files_ref->{qc_filter_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".qc_filter.machine.dat";
|
|
|
1404 }
|
|
|
1405
|
|
|
1406 sub define_coverage_uniformity_file_names {
|
|
|
1407 my $tag_ref = shift;
|
|
|
1408 my $parameters_ref = shift;
|
|
|
1409 my $files_ref = shift;
|
|
|
1410 $$files_ref->{coverage_uniformity_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".coverage_uniformity.dat";
|
|
|
1411 $$files_ref->{coverage_uniformity_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".coverage_uniformity.machine.dat";
|
|
|
1412 }
|
|
|
1413
|
|
|
1414 sub define_summary_file_names {
|
|
|
1415 my $tag_ref = shift;
|
|
|
1416 my $parameters_ref = shift;
|
|
|
1417 my $files_ref = shift;
|
|
|
1418 $$files_ref->{summary_file} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".summary.dat";
|
|
|
1419 $$files_ref->{summary_file_ps} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".summary.ps";
|
|
|
1420 $$files_ref->{summary_file_pdf} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".summary.pdf";
|
|
|
1421 $$files_ref->{summary_file_machine} = $$parameters_ref->{directory} . "/" . $$tag_ref . ".summary.machine.dat";
|
|
|
1422 }
|
