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annotate mafft/core/mccaskillwrap.c @ 18:e4d75f9efb90 draft

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planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #include "mltaln.h"
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2
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3 #define DEBUG 0
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4
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5 static char *whereismccaskillmea;
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6
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7 #ifdef enablemultithread
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8 typedef struct _thread_arg
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9 {
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10 int thread_no;
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11 int njob;
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12 int *jobpospt;
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13 int **gapmap;
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14 char **nogap;
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15 int nlenmax;
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16 RNApair ***pairprob;
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17 pthread_mutex_t *mutex;
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18 } thread_arg_t;
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19 #endif
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20
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21 void outmccaskill( FILE *fp, RNApair **pairprob, int length )
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22 {
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23 int i;
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24 RNApair *pt;
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25 for( i=0; i<length; i++ ) for( pt=pairprob[i]; pt->bestpos!=-1; pt++ )
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26 {
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27 if( pt->bestpos > i )
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28 fprintf( fp, "%d %d %50.40f\n", i, pt->bestpos, pt->bestscore );
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29 }
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30 }
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31
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32 #if 1
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33 static void readrawmccaskill( FILE *fp, RNApair **pairprob, int length )
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34 {
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35 char gett[1000];
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36 int *pairnum;
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37 int i;
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38 int left, right;
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39 float prob;
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40
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41 pairnum = (int *)calloc( length, sizeof( int ) );
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42 for( i=0; i<length; i++ ) pairnum[i] = 0;
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43
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44 while( 1 )
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45 {
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46 fgets( gett, 999, fp );
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47 if( feof( fp ) ) break;
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48 if( gett[0] == '>' ) continue;
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49 sscanf( gett, "%d %d %f", &left, &right, &prob );
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50 if( prob < 0.01 ) continue; // mxscarna to mafft ryoho ni eikyou
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51 //fprintf( stderr, "gett = %s\n", gett );
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52
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53 if( left != right && prob > 0.0 )
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54 {
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55 pairprob[left] = (RNApair *)realloc( pairprob[left], (pairnum[left]+2) * sizeof( RNApair ) );
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56 pairprob[left][pairnum[left]].bestscore = prob;
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57 pairprob[left][pairnum[left]].bestpos = right;
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58 pairnum[left]++;
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59 pairprob[left][pairnum[left]].bestscore = -1.0;
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60 pairprob[left][pairnum[left]].bestpos = -1;
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61 // fprintf( stderr, "%d-%d, %f\n", left, right, prob );
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62
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63 pairprob[right] = (RNApair *)realloc( pairprob[right], (pairnum[right]+2) * sizeof( RNApair ) );
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64 pairprob[right][pairnum[right]].bestscore = prob;
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65 pairprob[right][pairnum[right]].bestpos = left;
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66 pairnum[right]++;
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67 pairprob[right][pairnum[right]].bestscore = -1.0;
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68 pairprob[right][pairnum[right]].bestpos = -1;
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69 // fprintf( stderr, "%d-%d, %f\n", right, left, prob );
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70 }
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71 }
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72 free( pairnum );
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73 }
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74 #endif
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75
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76 #ifdef enablemultithread
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77 static void *athread( void *arg )
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78 {
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79 thread_arg_t *targ = (thread_arg_t *)arg;
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80 int thread_no = targ->thread_no;
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81 int njob = targ->njob;
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82 int *jobpospt = targ->jobpospt;
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83 int **gapmap = targ->gapmap;
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84 char **nogap = targ->nogap;
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85 int nlenmax = targ->nlenmax;
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86 RNApair ***pairprob = targ->pairprob;
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87
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88 int i, res;
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89 FILE *infp;
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90 char *com;
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91 char *dirname;
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92
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93 dirname = calloc( 100, sizeof( char ) );
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94 com = calloc( 1000, sizeof( char ) );
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95
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96
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97 while( 1 )
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98 {
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99 pthread_mutex_lock( targ->mutex );
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100 i = *jobpospt;
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101 if( i == njob )
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102 {
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103 pthread_mutex_unlock( targ->mutex );
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104 // return( NULL );
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105 break;
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106 }
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107 *jobpospt = i+1;
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108 pthread_mutex_unlock( targ->mutex );
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109
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110 commongappick_record( 1, nogap+i, gapmap[i] );
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111 if( strlen( nogap[i] ) == 0 ) continue;
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112
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113 sprintf( dirname, "_%d", i );
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114 sprintf( com, "rm -rf %s", dirname );
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115 system( com );
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116 sprintf( com, "mkdir %s", dirname );
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117 system( com );
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118
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119 fprintf( stderr, "%d / %d (by thread %4d)\n", i+1, njob, thread_no );
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120 sprintf( com, "%s/_mccaskillinorg", dirname );
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121 infp = fopen( com, "w" );
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122 // fprintf( infp, ">in\n%s\n", nogap[i] );
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123 fprintf( infp, ">in\n" );
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124 write1seq( infp, nogap[i] );
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125 fclose( infp );
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126
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127 sprintf( com, "tr -d '\\r' < %s/_mccaskillinorg > %s/_mccaskillin", dirname, dirname );
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128 system( com ); // for cygwin, wakaran
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129 if( alg == 'G' )
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130 sprintf( com, "cd %s; %s/dafs --mafft-out _mccaskillout _mccaskillin > _dum1 2>_dum", dirname, whereismccaskillmea );
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131 else
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132 sprintf( com, "cd %s; %s/mxscarnamod -m -writebpp _mccaskillin > _mccaskillout 2>_dum", dirname, whereismccaskillmea );
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133 res = system( com );
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134
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135 if( res )
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136 {
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137 fprintf( stderr, "ERROR IN mccaskill_mea\n" );
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138 exit( 1 );
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139 }
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140
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141 sprintf( com, "%s/_mccaskillout", dirname );
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142 infp = fopen( com, "r" );
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143 readrawmccaskill( infp, pairprob[i], nlenmax );
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144 fclose( infp );
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145
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146 sprintf( com, "rm -rf %s > /dev/null 2>&1", dirname );
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147 if( system( com ) )
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148 {
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149 fprintf( stderr, "retrying to rmdir\n" );
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150 // nanosleep( 100000 );
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151 sleep( 1 );
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152 system( com );
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153 }
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154 }
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155 free( dirname );
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156 free( com );
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157 return( NULL );
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158 }
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159 #endif
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160
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161 void arguments( int argc, char *argv[] )
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162 {
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163 int c;
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164 nthread = 1;
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165 inputfile = NULL;
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166 dorp = NOTSPECIFIED;
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167 kimuraR = NOTSPECIFIED;
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168 pamN = NOTSPECIFIED;
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169 whereismccaskillmea = NULL;
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170 alg = 's';
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171
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172 while( --argc > 0 && (*++argv)[0] == '-' )
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173 {
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174 while ( (c = *++argv[0]) )
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175 {
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176 switch( c )
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177 {
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178 case 'i':
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179 inputfile = *++argv;
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180 fprintf( stderr, "inputfile = %s\n", inputfile );
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181 --argc;
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182 goto nextoption;
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183 case 'd':
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184 whereismccaskillmea = *++argv;
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185 fprintf( stderr, "whereismccaskillmea = %s\n", whereismccaskillmea );
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186 --argc;
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187 goto nextoption;
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188 case 'C':
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189 nthread = myatoi( *++argv );
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190 fprintf( stderr, "nthread = %d\n", nthread );
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191 --argc;
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192 goto nextoption;
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193 case 's':
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194 alg = 's'; // use scarna; default
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195 break;
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196 case 'G':
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197 alg = 'G'; // use dafs, instead of scarna
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198 break;
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199 default:
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200 fprintf( stderr, "illegal option %c\n", c );
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201 argc = 0;
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202 break;
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203 }
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204 }
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205 nextoption:
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206 ;
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207 }
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208 if( argc != 0 )
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209 {
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210 fprintf( stderr, "options: Check source file !\n" );
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211 exit( 1 );
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212 }
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213 }
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214
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215
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216 int main( int argc, char *argv[] )
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217 {
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218 static char com[10000];
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219 static int *nlen;
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220 int left, right;
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221 int res;
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222 static char **name, **seq, **nogap;
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223 static int **gapmap;
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224 static int *order;
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225 int i, j;
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226 FILE *infp;
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227 RNApair ***pairprob;
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228 RNApair **alnpairprob;
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229 RNApair *pairprobpt;
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230 RNApair *pt;
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231 int *alnpairnum;
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232 float prob;
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233 int adpos;
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234
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235 arguments( argc, argv );
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236 #ifndef enablemultithread
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237 nthread = 0;
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238 #endif
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239
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240 if( inputfile )
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241 {
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242 infp = fopen( inputfile, "r" );
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243 if( !infp )
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244 {
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245 fprintf( stderr, "Cannot open %s\n", inputfile );
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246 exit( 1 );
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247 }
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248 }
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249 else
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250 infp = stdin;
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251
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252 if( !whereismccaskillmea )
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253 whereismccaskillmea = "";
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254
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255 getnumlen( infp );
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256 rewind( infp );
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257
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258 if( dorp != 'd' )
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259 {
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260 fprintf( stderr, "nuc only\n" );
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261 exit( 1 );
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262 }
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263
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264 seq = AllocateCharMtx( njob, nlenmax*2+1 );
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265 nogap = AllocateCharMtx( njob, nlenmax*2+1 );
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266 gapmap = AllocateIntMtx( njob, nlenmax*2+1 );
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267 order = AllocateIntVec( njob );
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268 name = AllocateCharMtx( njob, B+1 );
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269 nlen = AllocateIntVec( njob );
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270 pairprob = (RNApair ***)calloc( njob, sizeof( RNApair ** ) );
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271 alnpairprob = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
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272 alnpairnum = AllocateIntVec( nlenmax );
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273
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274 for( i=0; i<nlenmax; i++ ) alnpairnum[i] = 0;
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275
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276 readData_pointer( infp, name, nlen, seq );
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277 fclose( infp );
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278
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279 for( i=0; i<njob; i++ )
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280 {
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281 pairprob[i] = (RNApair **)calloc( nlenmax, sizeof( RNApair * ) );
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282 for( j=0; j<nlenmax; j++ )
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283 {
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284 pairprob[i][j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
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285 pairprob[i][j][0].bestpos = -1;
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286 pairprob[i][j][0].bestscore = -1.0;
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287 }
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288 strcpy( nogap[i], seq[i] );
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289 order[i] = i;
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290 }
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291 for( j=0; j<nlenmax; j++ )
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292 {
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293 alnpairprob[j] = (RNApair *)calloc( 1, sizeof( RNApair ) );
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294 alnpairprob[j][0].bestpos = -1;
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295 alnpairprob[j][0].bestscore = -1.0;
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296 }
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297
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298
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299 constants( njob, seq );
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300
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301 if( alg == 'G' )
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302 fprintf( stderr, "Running DAFS (Sato et al. 2012; http://www.ncrna.org/).\n" );
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303 else
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304 fprintf( stderr, "Running mxscarna with the mccaskill_mea mode.\n" );
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305 #ifdef enablemultithread
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306 if( nthread > 0 )
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307 {
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308 int jobpos;
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309 pthread_t *handle;
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310 pthread_mutex_t mutex;
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311 thread_arg_t *targ;
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312 jobpos = 0;
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313
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314 targ = calloc( nthread, sizeof( thread_arg_t ) );
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315 handle = calloc( nthread, sizeof( pthread_t ) );
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316 pthread_mutex_init( &mutex, NULL );
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317
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318 for( i=0; i<nthread; i++ )
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319 {
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320 targ[i].thread_no = i;
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321 targ[i].njob = njob;
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322 targ[i].jobpospt = &jobpos;
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323 targ[i].gapmap = gapmap;
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324 targ[i].nogap = nogap;
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325 targ[i].nlenmax = nlenmax;
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326 targ[i].pairprob = pairprob;
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327 targ[i].mutex = &mutex;
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328
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329 // athread( targ );
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330 pthread_create( handle+i, NULL, athread, (void *)(targ+i) );
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331
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332 }
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333
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334 for( i=0; i<nthread; i++ )
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335 {
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336 pthread_join( handle[i], NULL );
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337 }
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338 pthread_mutex_destroy( &mutex );
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339
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340 free( handle );
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341 free( targ );
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342
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343
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344 for( i=0; i<njob; i++ )
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345 {
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346 fprintf( stdout, ">%d\n", i );
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347 outmccaskill( stdout, pairprob[i], nlenmax );
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348 }
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349 }
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350 else
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351 #endif
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352 {
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353 for( i=0; i<njob; i++ )
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354 {
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355 fprintf( stderr, "%d / %d\n", i+1, njob );
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356 commongappick_record( 1, nogap+i, gapmap[i] );
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357 if( strlen( nogap[i] ) == 0 )
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358 {
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359 fprintf( stdout, ">%d\n", i );
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360 continue;
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361 }
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362
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363 infp = fopen( "_mccaskillinorg", "w" );
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364 // fprintf( infp, ">in\n%s\n", nogap[i] );
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365 fprintf( infp, ">in\n" );
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366 write1seq( infp, nogap[i] );
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367 fclose( infp );
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368
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369 system( "tr -d '\\r' < _mccaskillinorg > _mccaskillin" ); // for cygwin, wakaran
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370 if( alg == 'G' )
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371 sprintf( com, "env PATH=%s dafs --mafft-out _mccaskillout _mccaskillin > _dum1 2>_dum", whereismccaskillmea );
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372 else
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373 sprintf( com, "env PATH=%s mxscarnamod -m -writebpp _mccaskillin > _mccaskillout 2>_dum", whereismccaskillmea );
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374 res = system( com );
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375
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376 if( res )
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377 {
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378 fprintf( stderr, "ERROR IN mccaskill_mea\n" );
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379 exit( 1 );
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380 }
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381
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382 infp = fopen( "_mccaskillout", "r" );
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383 readrawmccaskill( infp, pairprob[i], nlenmax );
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384 fclose( infp );
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385 fprintf( stdout, ">%d\n", i );
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386 outmccaskill( stdout, pairprob[i], nlenmax );
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387 }
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388 }
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389
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390 for( i=0; i<njob; i++ )
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391 {
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392 for( j=0; j<nlen[i]; j++ ) for( pairprobpt=pairprob[i][j]; pairprobpt->bestpos!=-1; pairprobpt++ )
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393 {
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394 left = gapmap[i][j];
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395 right = gapmap[i][pairprobpt->bestpos];
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396 prob = pairprobpt->bestscore;
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397
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398 for( pt=alnpairprob[left]; pt->bestpos!=-1; pt++ )
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399 if( pt->bestpos == right ) break;
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400
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401 if( pt->bestpos == -1 )
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402 {
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403 alnpairprob[left] = (RNApair *)realloc( alnpairprob[left], (alnpairnum[left]+2) * sizeof( RNApair ) );
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404 adpos = alnpairnum[left];
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405 alnpairnum[left]++;
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406 alnpairprob[left][adpos].bestscore = 0.0;
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407 alnpairprob[left][adpos].bestpos = right;
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408 alnpairprob[left][adpos+1].bestscore = -1.0;
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409 alnpairprob[left][adpos+1].bestpos = -1;
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410 pt = alnpairprob[left]+adpos;
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411 }
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412 else
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413 adpos = pt-alnpairprob[left];
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414
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415 pt->bestscore += prob;
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416 if( pt->bestpos != right )
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417 {
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418 fprintf( stderr, "okashii!\n" );
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419 exit( 1 );
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420 }
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421 // fprintf( stderr, "adding %d-%d, %f\n", left, right, prob );
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422 }
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423 }
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424
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425 for( i=0; i<njob; i++ )
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426 {
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427 for( j=0; j<nlenmax; j++ ) free( pairprob[i][j] );
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428 free( pairprob[i] );
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429 }
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430 free( pairprob );
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431 for( j=0; j<nlenmax; j++ ) free( alnpairprob[j] );
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432 free( alnpairprob );
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433 free( alnpairnum );
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434 fprintf( stderr, "%d thread(s)\n", nthread );
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435 return( 0 );
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436
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437 #if 0
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438 fprintf( stdout, "result=\n" );
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439
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440 for( i=0; i<nlenmax; i++ ) for( pairprobpt=alnpairprob[i]; pairprobpt->bestpos!=-1; pairprobpt++ )
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441 {
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442 pairprobpt->bestscore /= (float)njob;
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443 left = i;
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444 right = pairprobpt->bestpos;
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445 prob = pairprobpt->bestscore;
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446 fprintf( stdout, "%d-%d, %f\n", left, right, prob );
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447 }
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448
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449 return( 0 );
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450 #endif
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451 }