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1 #include <stdio.h>
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2 #include <getopt.h>
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3 #include <vector>
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4 #include <pthread.h>
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5
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6 #include "alignments.hpp"
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7 #include "SubexonGraph.hpp"
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8 #include "SubexonCorrelation.hpp"
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9 #include "Constraints.hpp"
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10 #include "TranscriptDecider.hpp"
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11
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12 char usage[] = "./classes [OPTIONS]:\n"
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13 "Required:\n"
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14 "\t-s STRING: path to the subexon file.\n"
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15 "\t-b STRING: path to the BAM file.\n"
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16 "\t\tor\n"
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17 "\t--lb STRING: path to the file of the list of BAM files.\n"
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18 "Optional:\n"
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19 "\t-p INT: number of threads. (default: 1)\n"
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20 "\t-o STRING: the prefix of the output file. (default: not used)\n"
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21 "\t-c FLOAT: only use the subexons with classifier score <= than the given number. (default: 0.05)\n"
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22 "\t-f FLOAT: filter the transcript from the gene if its abundance is lower than the given number percent of the most abundant one. (default: 0.05)\n"
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23 "\t-d FLOAT: filter the transcript whose average read depth is less than the given number. (default: 2.5)\n"
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24 "\t--ls STRING: path to the file of the list of single-sample subexon files. (default: not used)\n"
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25 "\t--hasMateIdSuffix: the read id has suffix such as .1, .2 for a mate pair. (default: false)\n"
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26 "\t--maxDpConstraintSize: the maximum number of subexons a constraint can cover in dynamic programming. (default: 7; -1 for inf)\n"
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27 "\t--primaryParalog: use primary alignment to retain paralog genes instead of unique alignments. (default: not used)\n"
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28 ;
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29
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30 static const char *short_options = "s:b:f:o:d:p:c:h" ;
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31 static struct option long_options[] =
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32 {
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33 { "ls", required_argument, 0, 10000 },
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34 { "lb", required_argument, 0, 10001 },
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35 { "hasMateIdSuffix", no_argument, 0, 10002 },
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36 { "primaryParalog", no_argument, 0, 10003 },
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37 { "maxDpConstraintSize", required_argument, 0, 10004 },
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38 { (char *)0, 0, 0, 0}
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39 } ;
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40
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41 struct _getAlignmentsInfoThreadArg
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42 {
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43 std::vector<Alignments> *pAlignmentFiles ;
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44 int numThreads ;
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45 int tid ;
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46 } ;
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47
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48 struct _getConstraintsThreadArg
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49 {
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50 std::vector<Constraints> *pMultiSampleConstraints ;
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51 int numThreads ;
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52 int tid ;
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53
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54 struct _subexon *subexons ;
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55 int seCnt ;
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56 int start, end ;
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57 } ;
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58
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59 void *GetAlignmentsInfo_Thread( void *pArg )
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60 {
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61 int i ;
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62 std::vector <Alignments> &alignmentFiles = *( ( (struct _getAlignmentsInfoThreadArg *)pArg )->pAlignmentFiles ) ;
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63 int tid = ( (struct _getAlignmentsInfoThreadArg *)pArg )->tid ;
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64 int numThreads = ( (struct _getAlignmentsInfoThreadArg *)pArg )->numThreads ;
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65 int size = alignmentFiles.size() ;
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66 for ( i = 0 ; i < size ; ++i )
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67 {
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68 if ( i % numThreads == tid )
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69 {
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70 alignmentFiles[i].GetGeneralInfo( true ) ;
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71 alignmentFiles[i].Rewind() ;
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72 }
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73 }
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74
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75 pthread_exit( NULL ) ;
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76 }
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77
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78
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79 void *GetConstraints_Thread( void *pArg )
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80 {
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81 int i ;
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82 struct _getConstraintsThreadArg &arg = *( (struct _getConstraintsThreadArg *)pArg ) ;
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83 std::vector<Constraints> &multiSampleConstraints = *( arg.pMultiSampleConstraints ) ;
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84 int tid = arg.tid ;
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85 int numThreads = arg.numThreads ;
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86 int size = multiSampleConstraints.size() ;
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87 for ( i = 0 ; i < size ; ++i )
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88 {
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89 if ( i % numThreads == tid )
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90 multiSampleConstraints[i].BuildConstraints( arg.subexons, arg.seCnt, arg.start, arg.end ) ;
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91 }
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92 pthread_exit( NULL ) ;
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93 }
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94
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95 int main( int argc, char *argv[] )
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96 {
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97 int i, j ;
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98 int size ;
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99
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100 if ( argc <= 1 )
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101 {
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102 printf( "%s", usage ) ;
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103 return 0 ;
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104 }
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105
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106 int c, option_index ; // For getopt
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107 option_index = 0 ;
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108 FILE *fpSubexon = NULL ;
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109 double FPKMFraction = 0.05 ;
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110 double classifierThreshold ;
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111 double txptMinReadDepth = 2.5 ;
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112 char outputPrefix[1024] = "" ;
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113 int numThreads = 1 ;
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114 bool hasMateReadIdSuffix = false ;
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115 bool usePrimaryAsUnique = false ;
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116 int maxDpConstraintSize = 7 ;
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117
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118 std::vector<Alignments> alignmentFiles ;
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119 SubexonCorrelation subexonCorrelation ;
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120
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121 classifierThreshold = 0.05 ;
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122 while ( 1 )
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123 {
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124 c = getopt_long( argc, argv, short_options, long_options, &option_index ) ;
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125 if ( c == -1 )
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126 break ;
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127
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128 if ( c == 's' )
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129 {
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130 fpSubexon = fopen( optarg, "r" ) ;
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131 }
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132 else if ( c == 'b' )
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133 {
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134 Alignments a ;
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135 a.Open( optarg ) ;
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136 //a.SetAllowClip( false ) ;
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137 alignmentFiles.push_back( a ) ;
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138 }
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139 else if ( c == 'c' )
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140 {
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141 classifierThreshold = atof( optarg ) ;
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142 }
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143 else if ( c == 'f' )
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144 {
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145 FPKMFraction = atof( optarg ) ;
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146 }
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147 else if ( c == 'o' )
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148 {
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149 strcpy( outputPrefix, optarg ) ;
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150 }
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151 else if ( c == 'd' )
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152 {
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153 txptMinReadDepth = atof( optarg ) ;
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154 }
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155 else if ( c == 'p' )
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156 {
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157 numThreads = atoi( optarg ) ;
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158 }
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159 else if ( c == 10000 ) // the list of subexon files.
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160 {
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161 subexonCorrelation.Initialize( optarg ) ;
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162 }
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163 else if ( c == 10001 ) // the list of bam files.
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164 {
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165 FILE *fp = fopen( optarg, "r" ) ;
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166 char buffer[1024] ;
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167 while ( fgets( buffer, sizeof( buffer ), fp ) != NULL )
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168 {
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169 int len = strlen( buffer ) ;
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170 if ( buffer[len - 1] == '\n' )
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171 {
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172 buffer[len - 1] = '\0' ;
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173 --len ;
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174
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175 }
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176 Alignments a ;
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177 a.Open( buffer ) ;
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178 alignmentFiles.push_back( a ) ;
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179 }
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180 fclose( fp ) ;
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181 }
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182 else if ( c == 10002 ) // the mate pair read id has suffix.
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183 {
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184 hasMateReadIdSuffix = true ;
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185 }
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186 else if ( c == 10003 ) // do not check unique alignment
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187 {
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188 usePrimaryAsUnique = true ;
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189 }
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190 else if ( c == 10004 ) // maxDpConstraintSize
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191 {
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192 maxDpConstraintSize = atoi(optarg) ;
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193 }
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194 else
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195 {
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196 printf( "%s", usage ) ;
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197 exit( 1 ) ;
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198 }
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199 }
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200 if ( fpSubexon == NULL )
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201 {
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202 printf( "Cannot find combined subexon file.\n" ) ;
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203 exit( 1 ) ;
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204 }
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205 if ( alignmentFiles.size() < 1 )
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206 {
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207 printf( "Must use -b option to specify BAM files.\n" ) ;
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208 exit( 1 ) ;
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209 }
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210
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211
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212 if ( alignmentFiles.size() < 50 )
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213 {
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214 size = alignmentFiles.size() ;
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215 for ( i = 0 ; i < size ; ++i )
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216 {
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217 alignmentFiles[i].GetGeneralInfo( true ) ;
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218 alignmentFiles[i].Rewind() ;
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219 }
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220 }
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221 else
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222 {
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223 struct _getAlignmentsInfoThreadArg *args = new struct _getAlignmentsInfoThreadArg[ numThreads ] ;
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224 pthread_attr_t pthreadAttr ;
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225 pthread_t *threads ;
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226
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227 pthread_attr_init( &pthreadAttr ) ;
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228 pthread_attr_setdetachstate( &pthreadAttr, PTHREAD_CREATE_JOINABLE ) ;
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229
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230 threads = new pthread_t[ numThreads ] ;
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231
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232 for ( i = 0 ; i < numThreads ; ++i )
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233 {
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234 args[i].pAlignmentFiles = &alignmentFiles ;
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235 args[i].tid = i ;
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236 args[i].numThreads = numThreads ;
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237
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238 pthread_create( &threads[i], &pthreadAttr, GetAlignmentsInfo_Thread, &args[i] ) ;
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239 }
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240
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241 for ( i = 0 ; i < numThreads ; ++i )
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242 {
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243 pthread_join( threads[i], NULL ) ;
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244 }
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245
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246 pthread_attr_destroy( &pthreadAttr ) ;
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247 delete[] args ;
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248 delete[] threads ;
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249 }
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250
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251 // Build the subexon graph
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252 SubexonGraph subexonGraph( classifierThreshold, alignmentFiles[0], fpSubexon ) ;
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253 subexonGraph.ComputeGeneIntervals() ;
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254
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255 // Solve gene by gene
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256 int sampleCnt = alignmentFiles.size() ;
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257 std::vector<Constraints> multiSampleConstraints ;
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258 for ( i = 0 ; i < sampleCnt ; ++i )
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259 {
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260 Constraints constraints( &alignmentFiles[i] ) ;
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261 constraints.SetHasMateReadIdSuffix( hasMateReadIdSuffix ) ;
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262 constraints.SetUsePrimaryAsUnique( usePrimaryAsUnique ) ;
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263 multiSampleConstraints.push_back( constraints ) ;
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264 }
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265 MultiThreadOutputTranscript outputHandler( sampleCnt, alignmentFiles[0] ) ;
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266 outputHandler.SetOutputFPs( outputPrefix ) ;
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267
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268 if ( numThreads <= 1 )
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269 {
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270 TranscriptDecider transcriptDecider( FPKMFraction, classifierThreshold, txptMinReadDepth, sampleCnt, alignmentFiles[0] ) ;
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271
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272 transcriptDecider.SetMultiThreadOutputHandler( &outputHandler ) ;
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273 transcriptDecider.SetNumThreads( numThreads ) ;
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274 transcriptDecider.SetMaxDpConstraintSize( maxDpConstraintSize ) ;
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275
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276 int giCnt = subexonGraph.geneIntervals.size() ;
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277 for ( i = 0 ; i < giCnt ; ++i )
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278 {
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279 struct _geneInterval gi = subexonGraph.geneIntervals[i] ;
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280 struct _subexon *intervalSubexons = new struct _subexon[ gi.endIdx - gi.startIdx + 1 ] ;
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281 subexonGraph.ExtractSubexons( gi.startIdx, gi.endIdx, intervalSubexons ) ;
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282 printf( "%d: %d %s %d %d\n", i, gi.endIdx - gi.startIdx + 1,
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283 alignmentFiles[0].GetChromName( intervalSubexons[0].chrId ),
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284 gi.start + 1, gi.end + 1 ) ;
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285 fflush( stdout ) ;
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286
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287 subexonCorrelation.ComputeCorrelation( intervalSubexons, gi.endIdx - gi.startIdx + 1, alignmentFiles[0] ) ;
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288 for ( j = 0 ; j < sampleCnt ; ++j )
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289 multiSampleConstraints[j].BuildConstraints( intervalSubexons, gi.endIdx - gi.startIdx + 1, gi.start, gi.end ) ;
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290
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291 transcriptDecider.Solve( intervalSubexons, gi.endIdx - gi.startIdx + 1, multiSampleConstraints, subexonCorrelation ) ;
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292
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293 for ( j = 0 ; j < gi.endIdx - gi.startIdx + 1 ; ++j )
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294 {
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295 delete[] intervalSubexons[j].prev ;
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296 delete[] intervalSubexons[j].next ;
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297 }
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298 delete[] intervalSubexons ;
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299 }
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300 }
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301 else // multi-thread case.
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302 {
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303 --numThreads ; // one thread is used for read in the data.
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304
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305 // Allocate memory
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306 struct _transcriptDeciderThreadArg *pArgs = new struct _transcriptDeciderThreadArg[ numThreads ] ;
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307 pthread_mutex_t ftLock ;
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308 int *freeThreads ;
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309 int ftCnt ;
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310 pthread_cond_t fullWorkCond ;
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311 pthread_attr_t pthreadAttr ;
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312 pthread_t *threads ;
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313 pthread_t *getConstraintsThreads ;
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314 bool *initThreads ;
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315
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316 pthread_mutex_init( &ftLock, NULL ) ;
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317 pthread_cond_init( &fullWorkCond, NULL ) ;
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318 pthread_attr_init( &pthreadAttr ) ;
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319 pthread_attr_setdetachstate( &pthreadAttr, PTHREAD_CREATE_JOINABLE ) ;
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320
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321 threads = new pthread_t[ numThreads ] ;
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322 getConstraintsThreads = new pthread_t[ numThreads ] ;
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323 initThreads = new bool[numThreads] ;
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324 freeThreads = new int[ numThreads ] ;
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325 ftCnt = numThreads ;
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326 for ( i = 0 ; i < numThreads ; ++i )
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327 {
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328 pArgs[i].tid = i ;
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329 pArgs[i].sampleCnt = sampleCnt ;
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330 pArgs[i].numThreads = numThreads ;
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331 pArgs[i].maxDpConstraintSize = maxDpConstraintSize ;
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332 pArgs[i].FPKMFraction = FPKMFraction ;
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333 pArgs[i].classifierThreshold = classifierThreshold ;
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334 pArgs[i].txptMinReadDepth = txptMinReadDepth ;
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335 pArgs[i].alignments = &alignmentFiles[0] ;
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336 //pArgs[i].constraints = new std::vector<Constraints> ;
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337 pArgs[i].outputHandler = &outputHandler ;
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338
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339 freeThreads[i] = i ;
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340 pArgs[i].freeThreads = freeThreads ;
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341 pArgs[i].ftCnt = &ftCnt ;
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342 pArgs[i].ftLock = &ftLock ;
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343 pArgs[i].fullWorkCond = &fullWorkCond ;
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344
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345 for ( j = 0 ; j < sampleCnt ; ++j )
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346 {
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347 Constraints constraints( &alignmentFiles[j] ) ;
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348 pArgs[i].constraints.push_back( constraints ) ;
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349 }
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350
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351 initThreads[i] = false ;
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352 }
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353
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354
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355 // Read in and distribute the work
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356 int giCnt = subexonGraph.geneIntervals.size() ;
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357 for ( i = 0 ; i < giCnt ; ++i )
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358 {
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359 struct _geneInterval gi = subexonGraph.geneIntervals[i] ;
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360 struct _subexon *intervalSubexons = new struct _subexon[ gi.endIdx - gi.startIdx + 1 ] ;
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361 subexonGraph.ExtractSubexons( gi.startIdx, gi.endIdx, intervalSubexons ) ;
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362 subexonCorrelation.ComputeCorrelation( intervalSubexons, gi.endIdx - gi.startIdx + 1, alignmentFiles[0] ) ;
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363 printf( "%d: %d %s %d %d. Free threads: %d/%d\n", i, gi.endIdx - gi.startIdx + 1,
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364 alignmentFiles[0].GetChromName( intervalSubexons[0].chrId ),
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365 gi.start + 1, gi.end + 1, ftCnt, numThreads + 1 ) ;
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366 fflush( stdout ) ;
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367
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368 int gctCnt = ftCnt ;
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369 if ( gctCnt > 1 && sampleCnt > 1 )
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370 {
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371 gctCnt = ( gctCnt < sampleCnt ? gctCnt : sampleCnt ) ;
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372 struct _getConstraintsThreadArg *args = new struct _getConstraintsThreadArg[ gctCnt ] ;
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373 for ( j = 0 ; j < gctCnt ; ++j )
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374 {
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375 args[j].pMultiSampleConstraints = &multiSampleConstraints ;
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376 args[j].numThreads = gctCnt ;
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377 args[j].tid = j ;
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378 args[j].subexons = intervalSubexons ;
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379 args[j].seCnt = gi.endIdx - gi.startIdx + 1 ;
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380 args[j].start = gi.start ; args[j].end = gi.end ;
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381 pthread_create( &getConstraintsThreads[j], &pthreadAttr, GetConstraints_Thread, &args[j] ) ;
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382 }
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383
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384
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385
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386 for ( j = 0 ; j < gctCnt ; ++j )
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387 pthread_join( getConstraintsThreads[j], NULL ) ;
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388
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389 delete[] args ;
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390 }
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391 else
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392 {
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393 for ( j = 0 ; j < sampleCnt ; ++j )
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394 multiSampleConstraints[j].BuildConstraints( intervalSubexons, gi.endIdx - gi.startIdx + 1, gi.start, gi.end ) ;
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395 }
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396
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397 // Search for the free queue.
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398 int tag = -1 ; // get the working thread.
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399 pthread_mutex_lock( &ftLock ) ;
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400 if ( ftCnt == 0 )
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401 {
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402 pthread_cond_wait( &fullWorkCond, &ftLock ) ;
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403 }
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404 tag = freeThreads[ ftCnt - 1 ] ;
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405 --ftCnt ;
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406 pthread_mutex_unlock( &ftLock ) ;
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407
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408 if ( initThreads[tag] )
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409 pthread_join( threads[tag], NULL ) ; // Make sure the chosen thread exits.
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410
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411 // Assign the subexons, the constraints and correlation content.
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412 pArgs[tag].subexons = new struct _subexon[gi.endIdx - gi.startIdx + 1] ;
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413 pArgs[tag].seCnt = gi.endIdx - gi.startIdx + 1 ;
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414 for ( j = 0 ; j < pArgs[tag].seCnt ; ++j )
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415 {
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416 pArgs[tag].subexons[j] = intervalSubexons[j] ;
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417 int cnt = intervalSubexons[j].prevCnt ;
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418 pArgs[tag].subexons[j].prev = new int[cnt] ;
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419 memcpy( pArgs[tag].subexons[j].prev, intervalSubexons[j].prev, sizeof( int ) * cnt ) ;
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420 cnt = intervalSubexons[j].nextCnt ;
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421 pArgs[tag].subexons[j].next = new int[cnt] ;
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422 memcpy( pArgs[tag].subexons[j].next, intervalSubexons[j].next, sizeof( int ) * cnt ) ;
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423 }
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424
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425 for ( j = 0 ; j < sampleCnt ; ++j )
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426 {
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427 pArgs[tag].constraints[j].Assign( multiSampleConstraints[ j ] ) ;
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428 }
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429 pArgs[tag].subexonCorrelation.Assign( subexonCorrelation ) ;
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430 pthread_create( &threads[tag], &pthreadAttr, TranscriptDeciderSolve_Wrapper, &pArgs[tag] ) ;
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431 initThreads[tag] = true ;
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432 for ( j = 0 ; j < gi.endIdx - gi.startIdx + 1 ; ++j )
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433 {
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434 delete[] intervalSubexons[j].prev ;
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435 delete[] intervalSubexons[j].next ;
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436 }
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437 delete[] intervalSubexons ;
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438 }
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439
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440 for ( i = 0 ; i < numThreads ; ++i )
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441 {
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442 if ( initThreads[i] )
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443 pthread_join( threads[i], NULL ) ;
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444 }
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445
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446 // Release memory
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447 for ( i = 0 ; i < numThreads ; ++i )
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448 {
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449 std::vector<Constraints>().swap( pArgs[i].constraints ) ;
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450 }
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451 delete []pArgs ;
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452 pthread_attr_destroy( &pthreadAttr ) ;
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453 pthread_mutex_destroy( &ftLock ) ;
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454 pthread_cond_destroy( &fullWorkCond ) ;
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455
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456 delete[] threads ;
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457 delete[] getConstraintsThreads ;
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458 delete[] initThreads ;
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459 delete[] freeThreads ;
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460 } // end of else for multi-thread.
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|
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461
|
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462 outputHandler.OutputCommandInfo( argc, argv ) ;
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|
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463 for ( i = 0 ; i < sampleCnt ; ++i )
|
|
|
464 {
|
|
|
465 char buffer[1024] ;
|
|
|
466 alignmentFiles[i].GetFileName( buffer ) ;
|
|
|
467 int separator = -1 ;
|
|
|
468
|
|
|
469 // deprive the directory.
|
|
|
470 for ( j = 0 ; buffer[j] ; ++j )
|
|
|
471 {
|
|
|
472 if ( buffer[j] == '/' )
|
|
|
473 separator = j ;
|
|
|
474 }
|
|
|
475 if ( separator != -1 )
|
|
|
476 {
|
|
|
477 ++separator ;
|
|
|
478 for ( j = separator ; buffer[j] ; ++j )
|
|
|
479 buffer[j - separator] = buffer[j] ;
|
|
|
480 buffer[j - separator] = '\0' ;
|
|
|
481 }
|
|
|
482 outputHandler.OutputCommentToSampleGTF( i, buffer ) ;
|
|
|
483 }
|
|
|
484 outputHandler.ComputeFPKMTPM( alignmentFiles ) ;
|
|
|
485 outputHandler.Flush() ;
|
|
|
486
|
|
|
487 for ( i = 0 ; i < sampleCnt ; ++i )
|
|
|
488 alignmentFiles[i].Close() ;
|
|
|
489 fclose( fpSubexon ) ;
|
|
|
490 return 0 ;
|
|
|
491 }
|
