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annotate mafft/core/dndfast7.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 #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 inputfile = NULL;
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33 disopt = 0;
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34 divpairscore = 0;
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35 swopt = "";
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36
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37 while( --argc > 0 && (*++argv)[0] == '-' )
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38 {
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39 while ( (c = *++argv[0]) )
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40 {
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41 switch( c )
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42 {
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43 case 'i':
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44 inputfile = *++argv;
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45 fprintf( stderr, "inputfile = %s\n", inputfile );
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46 --argc;
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47 goto nextoption;
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48 case 'I':
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49 disopt = 1;
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50 break;
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51 case 'A':
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52 swopt = "-A";
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53 break;
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54 default:
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55 fprintf( stderr, "illegal option %c\n", c );
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56 argc = 0;
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57 break;
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58 }
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59 }
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60 nextoption:
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61 ;
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62 }
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63 if( argc != 0 )
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64 {
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65 fprintf( stderr, "options: -i\n" );
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66 exit( 1 );
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67 }
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68 }
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69
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70 int main( int argc, char *argv[] )
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71 {
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72 int ktuple;
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73 int i, j;
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74 FILE *hat2p;
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75 FILE *hat3p;
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76 FILE *infp;
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77 char **seq = NULL; // by D.Mathog
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78 char **seq1;
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79 char **name;
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80 char **name1;
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81 static int nlen1[M];
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82 double **mtx;
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83 double **mtx2;
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84 static int nlen[M];
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85 static char b[B];
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86 double max;
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87 char com[1000];
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88 int opt[M];
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89 int res;
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90 char *home;
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91 char *fastapath;
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92 char queryfile[B];
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93 char datafile[B];
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94 char fastafile[B];
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95 char hat2file[B];
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96 int pid = (int)getpid();
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97 LocalHom **localhomtable, *tmpptr;
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98 #if 0
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99 home = getenv( "HOME" );
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100 #else /* $HOME wo tsukau to fasta ni watasu hikisuu ga afureru */
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101 home = NULL;
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102 #endif
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103 fastapath = getenv( "FASTA_4_MAFFT" );
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104 if( !fastapath )
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105 fastapath = "fasta34";
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106
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107 #if DEBUG
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108 if( home ) fprintf( stderr, "home = %s\n", home );
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109 #endif
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110 if( !home ) home = "";
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111 sprintf( queryfile, "%s/tmp/query-%d", home, pid );
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112 sprintf( datafile, "%s/tmp/data-%d", home, pid );
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113 sprintf( fastafile, "%s/tmp/fasta-%d", home, pid );
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114 sprintf( hat2file, "hat2-%d", pid );
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115
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116
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117 arguments( argc, argv );
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118
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119 if( inputfile )
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120 {
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121 infp = fopen( inputfile, "r" );
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122 if( !infp )
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123 {
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124 fprintf( stderr, "Cannot open %s\n", inputfile );
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125 exit( 1 );
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126 }
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127 }
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128 else
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129 infp = stdin;
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130
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131
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132
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133 #if 0
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134 PreRead( stdin, &njob, &nlenmax );
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135 #else
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136 dorp = NOTSPECIFIED;
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137 getnumlen( infp );
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138 #endif
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139
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140 if( dorp == 'd' )
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141 {
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142 scoremtx = -1;
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143 pamN = NOTSPECIFIED;
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144 }
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145 else
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146 {
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147 nblosum = 62;
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148 scoremtx = 1;
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149 }
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150 constants( njob, seq );
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151
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152 rewind( infp );
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153
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154 name = AllocateCharMtx( njob, B+1 );
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155 name1 = AllocateCharMtx( njob, B+1 );
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156 seq = AllocateCharMtx( njob, nlenmax+1 );
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157 seq1 = AllocateCharMtx( 2, nlenmax+1 );
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158 mtx = AllocateDoubleMtx( njob, njob );
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159 mtx2 = AllocateDoubleMtx( njob, njob );
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160 localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
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161 for( i=0; i<njob; i++)
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162 {
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163 localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
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164 for( j=0; j<njob; j++)
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165 {
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166 localhomtable[i][j].start1 = -1;
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167 localhomtable[i][j].end1 = -1;
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168 localhomtable[i][j].start2 = -1;
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169 localhomtable[i][j].end2 = -1;
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170 localhomtable[i][j].opt = -1.0;
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171 localhomtable[i][j].next = NULL;
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172 }
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173 }
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174
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175 #if 0
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176 FRead( infp, name, nlen, seq );
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177 #else
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178 readData_pointer( infp, name, nlen, seq );
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179 #endif
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180 fclose( infp );
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181
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182 if( scoremtx == -1 ) ktuple = 6;
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183 else ktuple = 1;
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184
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185 for( i=0; i<njob; i++ )
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186 {
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187 gappick0( seq1[0], seq[i] );
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188 strcpy( seq[i], seq1[0] );
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189 }
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190 for( j=0; j<njob; j++ )
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191 {
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192 sprintf( name1[j], "+==========+%d ", j );
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193 nlen1[j] = nlen[j];
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194 }
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195 hat2p = fopen( datafile, "w" );
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196 if( !hat2p ) ErrorExit( "Cannot open datafile." );
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197 WriteForFasta( hat2p, njob, name1, nlen1, seq );
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198 fclose( hat2p );
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199
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200 for( i=0; i<njob; i++ )
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201 {
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202 // fprintf( stderr, "### i = %d\n", i );
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203 hat2p = fopen( datafile, "w" );
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204 if( !hat2p ) ErrorExit( "Cannot open datafile." );
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205 WriteForFasta( hat2p, njob-i, name1+i, nlen1+i, seq+i );
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206 fclose( hat2p );
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207
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208 seq1[0] = seq[i];
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209 nlen1[0] = nlen[i];
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210
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211 hat2p = fopen( queryfile, "w" );
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212 if( !hat2p ) ErrorExit( "Cannot open queryfile." );
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213 WriteForFasta( hat2p, 1, name1+i, nlen1, seq1 );
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214 fclose( hat2p );
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215
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216
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217 if( scoremtx == -1 )
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218 sprintf( com, "%s %s -z3 -m10 -n -Q -b%d -E%d -d%d %s %s %d > %s", fastapath, swopt, M, M, M, queryfile, datafile, ktuple, fastafile );
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219 else
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220 sprintf( com, "%s %s -z3 -m10 -Q -b%d -E%d -d%d %s %s %d > %s", fastapath, swopt, M, M, M, queryfile, datafile, ktuple, fastafile );
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221 res = system( com );
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222 if( res ) ErrorExit( "error in fasta" );
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223
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224
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225
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226 hat2p = fopen( fastafile, "r" );
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227 if( hat2p == NULL )
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228 ErrorExit( "file 'fasta.$$' does not exist\n" );
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229 if( scoremtx == -1 )
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230 res = ReadFasta34m10_nuc( hat2p, mtx[i], i, name1, localhomtable[i] );
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231 else
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232 res = ReadFasta34m10( hat2p, mtx[i], i, name1, localhomtable[i] );
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233 fclose( hat2p );
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234
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235 if( res < njob - i )
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236 {
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237 fprintf( stderr, "count (fasta34 -z 3) = %d\n", res );
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238 exit( 1 );
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239 }
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240
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241
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242 if( i == 0 )
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243 for( j=0; j<njob; j++ ) opt[j] = (int)mtx[0][j];
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244
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245
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246 #if 0
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247 {
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248 int ii, jj;
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249 if( i < njob-1 ) for( jj=i; jj<i+5; jj++ )
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250 fprintf( stdout, "mtx[%d][%d] = %f\n", i+1, jj+1, mtx[i][jj] );
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251 }
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252 #endif
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253 fprintf( stderr, "query : %4d / %5d\r", i+1, njob );
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254 }
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255
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256 for( i=0; i<njob; i++ )
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257 {
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258 max = mtx[i][i];
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259 if( max == 0.0 )
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260 {
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261 for( j=0; j<njob; j++ )
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262 mtx2[i][j] = 2.0;
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263 }
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264 else
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265 {
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266 for( j=0; j<njob; j++ )
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267 {
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268 // fprintf( stderr, "##### mtx[%d][%d] = %f\n", i, j, mtx[i][j] );
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269 mtx2[i][j] = ( max - mtx[MIN(i,j)][MAX(i,j)] ) / max * 2.0;
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270 // 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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271 }
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272 }
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273 }
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274 for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
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275 {
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276 // fprintf( stdout, "mtx2[%d][%d] = %f, %f\n", i+1, j+1, mtx2[i][j], mtx2[j][i] );
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277 mtx2[i][j] = MIN( mtx2[i][j], mtx2[j][i] );
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278 }
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279
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280 #if 0
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281 {
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282 int ii, jj;
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283 if( i < njob-1 ) for( jj=i+1; jj<njob; jj++ )
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284 fprintf( stderr, "mtx2[][] = %f\n", mtx2[i][jj] );
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285 }
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286 #endif
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287
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288 for( i=0; i<njob; i++ ) name[i][0] = '=';
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289
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290 if( disopt )
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291 {
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292 strcpy( b, name[0] );
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293 sprintf( name[0], "=query====lgth=%04d-%04d %.*s", nlen[0], howmanyx( seq[0] ), B-30, b );
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294 #if 0
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295 strins( b, name[0] );
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296 #endif
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297 for( i=1; i<njob; i++ )
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298 {
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299 strcpy( b, name[i] );
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300 sprintf( name[i], "=opt=%04d=lgth=%04d-%04d %.*s", opt[i], nlen[i], howmanyx( seq[i] ), B-30, b );
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301 #if 0
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302 strins( b, name[i] );
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303 #endif
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304 }
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305 }
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306
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307 hat2p = fopen( hat2file, "w" );
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308 if( !hat2p ) ErrorExit( "Cannot open hat2." );
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309 WriteHat2_pointer( hat2p, njob, name, mtx2 );
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310 fclose( hat2p );
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311
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312 #if 1
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313 fprintf( stderr, "##### writing hat3\n" );
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314 hat3p = fopen( "hat3", "w" );
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315 if( !hat3p ) ErrorExit( "Cannot open hat3." );
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316 for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
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317 {
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318 for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
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319 {
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320 if( tmpptr->opt == -1.0 ) continue;
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321 fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d %p\n", i, j, tmpptr->overlapaa, tmpptr->opt, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2, (void *)tmpptr->next );
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322 }
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323 }
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324 fclose( hat3p );
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325 #endif
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326
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327 sprintf( com, "/bin/rm %s %s %s", queryfile, datafile, fastafile );
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328 system( com );
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329
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330 #if 0
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331 sprintf( com, ALNDIR "/supgsdl < %s", hat2file );
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332 res = system( com );
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333 if( res ) ErrorExit( "error in spgsdl" );
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334 #endif
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335
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336 sprintf( com, "mv %s hat2", hat2file );
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337 res = system( com );
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338 if( res ) ErrorExit( "error in mv" );
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339
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340 SHOWVERSION;
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341 exit( 0 );
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342 }