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annotate mafft/core/dndfast4.c @ 18:e4d75f9efb90 draft

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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 #include <sys/types.h>
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3 #include <unistd.h>
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4 #define DEBUG 0
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5 #define TEST 0
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6
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7
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8 int howmanyx( char *s )
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9 {
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10 int val = 0;
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11 if( scoremtx == -1 )
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12 {
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13 do
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14 {
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15 if( !strchr( "atgcuATGCU", *s ) ) val++;
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16 } while( *++s );
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17 }
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18 else
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19 {
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20 do
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21 {
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22 if( !strchr( "ARNDCQEGHILKMFPSTWYV", *s ) ) val++;
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23 } while( *++s );
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24 }
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25 return( val );
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26 }
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27
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28 void arguments( int argc, char *argv[] )
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29 {
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30 int c;
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31
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32 disopt = 0;
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33
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34 while( --argc > 0 && (*++argv)[0] == '-' )
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35 while ( c = *++argv[0] )
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36 switch( c )
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37 {
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38 case 'i':
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39 disopt = 1;
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40 break;
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41 default:
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42 fprintf( stderr, "illegal option %c\n", c );
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43 argc = 0;
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44 break;
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45 }
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46 if( argc != 0 )
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47 {
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48 fprintf( stderr, "options: -i\n" );
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49 exit( 1 );
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50 }
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51 }
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52
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53 int main( int argc, char *argv[] )
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54 {
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55 int ktuple;
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56 int i, j;
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57 FILE *hat2p;
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58 char **seq;
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59 char **seq1;
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60 static char name[M][B];
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61 static char name1[M][B];
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62 static int nlen1[M];
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63 double **mtx;
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64 double **mtx2;
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65 static int nlen[M];
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66 char b[B];
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67 double max;
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68 char com[B];
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69 int opt[M];
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70 int res;
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71 char *home;
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72 char queryfile[B];
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73 char datafile[B];
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74 char fastafile[B];
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75 char hat2file[B];
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76 int pid = (int)getpid();
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77 #if 0
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78 home = getenv( "HOME" );
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79 #else /* $HOME wo tsukau to fasta ni watasu hikisuu ga afureru */
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80 home = NULL;
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81 #endif
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82
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83 #if DEBUG
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84 if( home ) fprintf( stderr, "home = %s\n", home );
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85 #endif
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86 if( !home ) home = "";
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87 sprintf( queryfile, "%s/tmp/query-%d\0", home, pid );
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88 sprintf( datafile, "%s/tmp/data-%d\0", home, pid );
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89 sprintf( fastafile, "%s/tmp/fasta-%d\0", home, pid );
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90 sprintf( hat2file, "hat2-%d\0", pid );
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91
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92 arguments( argc, argv );
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93 #if 0
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94 PreRead( stdin, &njob, &nlenmax );
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95 #else
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96 getnumlen( stdin );
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97 #endif
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98 rewind( stdin );
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99
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100 seq = AllocateCharMtx( njob, nlenmax+1 );
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101 seq1 = AllocateCharMtx( 2, nlenmax+1 );
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102 mtx = AllocateDoubleMtx( njob, njob );
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103 mtx2 = AllocateDoubleMtx( njob, njob );
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104
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105 #if 0
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106 FRead( stdin, name, nlen, seq );
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107 #else
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108 readData( stdin, name, nlen, seq );
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109 #endif
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110 if( scoremtx == -1 ) ktuple = 6;
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111 else ktuple = 1;
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112
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113 for( i=0; i<njob; i++ )
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114 {
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115 gappick0( seq1[0], seq[i] );
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116 strcpy( seq[i], seq1[0] );
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117 }
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118 for( j=0; j<njob; j++ )
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119 {
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120 sprintf( name1[j], "+==========+%d \0", j );
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121 nlen1[j] = nlen[j];
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122 }
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123 hat2p = fopen( datafile, "w" );
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124 if( !hat2p ) ErrorExit( "Cannot open datafile." );
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125 WriteForFasta( hat2p, njob, name1, nlen1, seq );
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126 fclose( hat2p );
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127
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128 for( i=0; i<njob; i++ )
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129 {
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130
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131 hat2p = fopen( datafile, "w" );
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132 if( !hat2p ) ErrorExit( "Cannot open datafile." );
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133 WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
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134 fclose( hat2p );
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135
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136
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137 seq1[0] = seq[i];
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138 nlen1[0] = nlen[i];
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139
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140 hat2p = fopen( queryfile, "w" );
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141 if( !hat2p ) ErrorExit( "Cannot open queryfile." );
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142 WriteForFasta( hat2p, 1, name1+i, nlen1, seq1 );
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143 fclose( hat2p );
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144
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145 if( scoremtx == -1 )
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146 sprintf( com, "fasta3 -n -Q -h -b%d -E%d -d%d %s %s %d > %s\0", M, M, 0, queryfile, datafile, ktuple, fastafile );
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147 else
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148 sprintf( com, "fasta3 -Q -h -b%d -E%d -d%d %s %s %d > %s\0", M, M, 0, queryfile, datafile, ktuple, fastafile );
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149 res = system( com );
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150 if( res ) ErrorExit( "error in fasta" );
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151
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152 hat2p = fopen( fastafile, "r" );
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153 if( hat2p == NULL )
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154 ErrorExit( "file 'fasta.$$' does not exist\n" );
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155 ReadFasta3( hat2p, mtx[i], njob-i, name1 );
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156
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157 if( i == 0 )
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158 for( j=0; j<njob; j++ ) opt[j] = (int)mtx[0][j];
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159
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160 fclose( hat2p );
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161
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162 #if 1
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163 {
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164 int ii, jj;
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165 if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
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166 fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
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167 }
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168 #endif
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169 fprintf( stderr, "query : %#4d\n", i+1 );
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170 }
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171
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172 for( i=0; i<njob; i++ )
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173 {
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174 max = mtx[i][i];
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175 if( max == 0.0 )
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176 {
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177 for( j=0; j<njob; j++ )
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178 mtx2[i][j] = 2.0;
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179 }
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180 else
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181 {
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182 for( j=0; j<njob; j++ )
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183 {
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184 mtx2[i][j] = ( max - mtx[MIN(i,j)][MAX(i,j)] ) / max * 2.0;
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185 // fprintf( stdout, "max = %f, mtx[%d][%d] = %f -> %f\n", max, i+1, j+1, mtx[i][j], mtx2[i][j] );
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186 }
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187 }
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188 }
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189 for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
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190 {
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191 // fprintf( stdout, "mtx2[%d][%d] = %f, %f\n", i+1, j+1, mtx2[i][j], mtx2[j][i] );
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192 mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
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193 }
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194 #if 0
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195 {
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196 int ii, jj;
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197 if( i < njob-1 ) for( jj=i+1; jj<njob; jj++ )
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198 fprintf( stderr, "mtx2[][] = %f\n", mtx2[i][jj] );
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199 }
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200 #endif
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201
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202 for( i=0; i<njob; i++ ) name[i][0] = '=';
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203
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204 if( disopt )
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205 {
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206 strcpy( b, name[0] );
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207 sprintf( name[0], "=query====lgth=%#04d-%04d %.*s\0", nlen[0], howmanyx( seq[0] ), B-30, b );
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208 #if 0
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209 strins( b, name[0] );
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210 #endif
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211 for( i=1; i<njob; i++ )
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212 {
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213 strcpy( b, name[i] );
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214 sprintf( name[i], "=opt=%#04d=lgth=%#04d-%04d %.*s\0", opt[i], nlen[i], howmanyx( seq[i] ), B-30, b );
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215 #if 0
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216 strins( b, name[i] );
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217 #endif
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218 }
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219 }
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220
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221 hat2p = fopen( hat2file, "w" );
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222 if( !hat2p ) ErrorExit( "Cannot open hat2." );
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223 WriteHat2( hat2p, njob, name, mtx2 );
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224 fclose( hat2p );
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225
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226 sprintf( com, "/bin/rm %s %s %s", queryfile, datafile, fastafile );
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227 system( com );
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228
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229 #if 0
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230 sprintf( com, ALNDIR "/supgsdl < %s\0", hat2file );
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231 res = system( com );
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232 if( res ) ErrorExit( "error in spgsdl" );
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233 #endif
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234
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235 sprintf( com, "mv %s hat2", hat2file );
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236 res = system( com );
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237 if( res ) ErrorExit( "error in mv" );
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238
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239 SHOWVERSION;
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240 exit( 0 );
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241 }