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annotate mafft/core/getlag.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
parents
children
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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 #define IODEBUG 0
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5
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6 void arguments( int argc, char *argv[] )
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7 {
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8 int c;
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9
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10 calledByXced = 0;
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11 devide = 0;
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12 use_fft = 0;
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13 fftscore = 1;
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14 fftRepeatStop = 0;
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15 fftNoAnchStop = 0;
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16 weight = 3;
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17 utree = 1;
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18 tbutree = 1;
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19 refine = 0;
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20 check = 1;
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21 cut = 0.0;
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22 disp = 0;
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23 outgap = 1;
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24 alg = 'C';
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25 mix = 0;
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26 tbitr = 0;
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27 scmtd = 5;
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28 tbweight = 0;
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29 tbrweight = 3;
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30 checkC = 0;
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31 treemethod = 'x';
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32 contin = 0;
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33 ppenalty = NOTSPECIFIED;
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34 ppenalty_ex = NOTSPECIFIED;
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35 poffset = NOTSPECIFIED;
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36 kimuraR = NOTSPECIFIED;
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37 pamN = NOTSPECIFIED;
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38 geta2 = GETA2;
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39 scoremtx = NOTSPECIFIED;
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40
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41 while( --argc > 0 && (*++argv)[0] == '-' )
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42 {
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43 while ( (c = *++argv[0]) )
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44 {
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45 switch( c )
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46 {
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47 case 'f':
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48 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
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49 fprintf( stderr, "ppenalty = %d\n", ppenalty );
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50 --argc;
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51 goto nextoption;
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52 case 'g':
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53 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
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54 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
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55 --argc;
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56 goto nextoption;
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57 case 'h':
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58 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
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59 fprintf( stderr, "poffset = %d\n", poffset );
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60 --argc;
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61 goto nextoption;
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62 case 'D':
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63 scoremtx = -1;
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64 break;
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65 case 'P':
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66 scoremtx = 0;
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67 break;
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68 case 'i':
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69 contin = 1;
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70 break;
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71 case 'e':
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72 fftscore = 0;
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73 break;
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74 case 'O':
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75 fftNoAnchStop = 1;
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76 break;
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77 case 'R':
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78 fftRepeatStop = 1;
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79 break;
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80 case 'Q':
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81 calledByXced = 1;
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82 break;
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83 case 's':
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84 treemethod = 's';
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85 break;
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86 case 'x':
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87 treemethod = 'x';
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88 break;
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89 case 'p':
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90 treemethod = 'p';
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91 break;
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92 case 'a':
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93 alg = 'a';
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94 break;
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95 case 'A':
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96 alg = 'A';
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97 break;
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98 case 'S':
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99 alg = 'S';
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100 break;
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101 case 'C':
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102 alg = 'C';
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103 break;
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104 case 'F':
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105 use_fft = 1;
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106 break;
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107 case 'v':
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108 tbrweight = 3;
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109 break;
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110 case 'd':
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111 disp = 1;
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112 break;
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113 case 'o':
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114 outgap = 0;
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115 break;
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116 /* Modified 01/08/27, default: user tree */
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117 case 'J':
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118 tbutree = 0;
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119 break;
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120 /* modification end. */
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121 case 'Z':
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122 checkC = 1;
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123 break;
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124 default:
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125 fprintf( stderr, "illegal option %c\n", c );
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126 argc = 0;
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127 break;
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128 }
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129 }
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130 nextoption:
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131 ;
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132 }
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133 if( argc == 1 )
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134 {
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135 cut = atof( (*argv) );
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136 argc--;
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137 }
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138 if( argc != 0 )
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139 {
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140 fprintf( stderr, "options: Check source file !\n" );
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141 exit( 1 );
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142 }
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143 if( tbitr == 1 && outgap == 0 )
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144 {
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145 fprintf( stderr, "conflicting options : o, m or u\n" );
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146 exit( 1 );
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147 }
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148 if( alg == 'C' && outgap == 0 )
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149 {
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150 fprintf( stderr, "conflicting options : C, o\n" );
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151 exit( 1 );
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152 }
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153 readOtherOptions( &ppid, &fftThreshold, &fftWinSize );
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154 }
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155
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156
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157 void treebase( char **name, int nlen[M], char **seq, char **aseq, char **mseq1, char **mseq2, double **mtx, int ***topol, double **len, double **eff, int alloclen )
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158 {
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159 int i, j, l;
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160 int clus1, clus2;
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161 int s1, s2, r1, r2;
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162 float pscore;
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163 static char *indication1, *indication2;
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164 static char **name1, **name2;
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165 static double **partialmtx = NULL;
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166 static int ***partialtopol = NULL;
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167 static double **partiallen = NULL;
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168 static double **partialeff = NULL;
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169 static double *effarr = NULL;
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170 static double *effarr1 = NULL;
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171 static double *effarr2 = NULL;
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172 #if 0
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173 char pair[njob][njob];
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174 #else
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175 static char **pair;
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176 #endif
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177 if( partialtopol == NULL )
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178 {
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179 partialmtx = AllocateDoubleMtx( njob, njob );
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180 partialtopol = AllocateIntCub( njob, 2, njob );
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181 partialeff = AllocateDoubleMtx( njob, njob );
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182 partiallen = AllocateDoubleMtx( njob, 2 );
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183 effarr = AllocateDoubleVec( njob );
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184 effarr1 = AllocateDoubleVec( njob );
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185 effarr2 = AllocateDoubleVec( njob );
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186 indication1 = AllocateCharVec( njob*3+100 );
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187 indication2 = AllocateCharVec( njob*3+100 );
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188 name1 = AllocateCharMtx( njob, B+1 );
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189 name2 = AllocateCharMtx( njob, B+1 );
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190 #if 0
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191 #else
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192 pair = AllocateCharMtx( njob, njob );
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193 #endif
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194 }
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195
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196 if( checkC )
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197 for( i=0; i<njob; i++ ) fprintf( stderr, "eff in tb-%d %f\n", i, eff[i][i] );
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198
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199 for( i=0; i<njob; i++ ) effarr[i] = eff[i][i];
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200 for( i=0; i<njob; i++ ) strcpy( aseq[i], seq[i] );
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201
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202 if( checkC )
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203 for( i=0; i<njob; i++ ) fprintf( stderr, "effarr for aseq-%d %f\n", i, effarr[i] );
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204
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205 writePre( njob, name, nlen, aseq, 0 );
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206
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207 for( i=0; i<njob; i++ ) for( j=0; j<njob; j++ ) pair[i][j] = 0;
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208 for( i=0; i<njob; i++ ) pair[i][i] = 1;
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209 for( l=0; l<njob-1; l++ )
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210 {
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211 s1 = topol[l][0][0];
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212 for( i=0; (r1=topol[l][0][i])>-1; i++ )
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213 if( pair[s1][r1] != 1 ) exit( 1 );
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214 s2 = topol[l][1][0];
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215 for( i=0; (r2=topol[l][1][i])>-1; i++ )
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216 if( pair[s2][r2] != 1 ) exit( 1 );
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217
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218 clus1 = conjuction( pair, s1, aseq, mseq1, effarr1, effarr, name, name1, indication1 );
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219 clus2 = conjuction( pair, s2, aseq, mseq2, effarr2, effarr, name, name2, indication2 );
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220 fprintf( trap_g, "\nSTEP-%d\n", l );
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221 fprintf( trap_g, "group1 = %s\n", indication1 );
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222 fprintf( trap_g, "group2 = %s\n", indication2 );
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223
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224 fprintf( stderr, "STEP %d /%d\n", l+1, njob-1 );
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225 fprintf( stderr, "group1 = %.66s", indication1 );
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226 if( strlen( indication1 ) > 66 ) fprintf( stderr, "..." );
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227 fprintf( stderr, "\n" );
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228 fprintf( stderr, "group2 = %.66s", indication2 );
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229 if( strlen( indication2 ) > 66 ) fprintf( stderr, "..." );
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230 fprintf( stderr, "\n" );
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231
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232 if( checkC )
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233 for( i=0; i<clus1; i++ ) fprintf( stderr, "STEP%d-eff for mseq1-%d %f\n", l+1, i, effarr1[i] );
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234 /*
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235 fprintf( stderr, "before align all\n" );
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236 display( aseq, njob );
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237 fprintf( stderr, "\n" );
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238 fprintf( stderr, "before align 1 %s \n", indication1 );
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239 display( mseq1, clus1 );
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240 fprintf( stderr, "\n" );
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241 fprintf( stderr, "before align 2 %s \n", indication2 );
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242 display( mseq2, clus2 );
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243 fprintf( stderr, "\n" );
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244 */
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245
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246 pscore = Fgetlag( n_dis_consweight_multi, mseq1, mseq2, effarr1, effarr2, clus1, clus2, alloclen );
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247
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248 for( i=0; (r2=topol[l][1][i])>-1; i++ )
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249 {
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250 pair[s1][r2] = 1;
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251 pair[s2][r2] = 0;
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252 }
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253
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254 writePre( njob, name, nlen, aseq, 0 );
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255
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256 if( disp ) display( aseq, njob );
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257 fprintf( stderr, "\n" );
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258
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259 }
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260 }
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261
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262 static void WriteOptions( FILE *fp )
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263 {
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264 fprintf( fp, "tree-base method\n" );
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265 if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
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266 else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
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267 if( tbitr || tbweight )
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268 {
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269 fprintf( fp, "iterate at each step\n" );
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270 if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
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271 if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
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272 if( tbweight ) fprintf( fp, " weighted\n" );
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273 fprintf( fp, "\n" );
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274 }
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275 if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
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276 else if( scoremtx == 1 ) fprintf( fp, "Dayhoff( machigai ga aru )\n" );
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277 else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
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278 else if( scoremtx == -1 ) fprintf( fp, "DNA\n" );
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279
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280 if( scoremtx == 0 || scoremtx == -1 )
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281 fprintf( fp, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
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282 else
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283 fprintf( fp, "Gap Penalty = %+5.2f\n", (double)ppenalty/1000 );
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284
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285 if( alg == 'a' )
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286 fprintf( fp, "Algorithm A\n" );
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287 else if( alg == 'A' )
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288 fprintf( fp, "Apgorithm A+\n" );
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289 else if( alg == 'S' )
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290 fprintf( fp, "Apgorithm S\n" );
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291 else if( alg == 'C' )
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292 fprintf( fp, "Apgorithm A+/C\n" );
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293 else
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294 fprintf( fp, "Unknown algorithm\n" );
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295
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296 if( treemethod == 'x' )
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297 fprintf( fp, "Tree = UPGMA (3).\n" );
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298 else if( treemethod == 's' )
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299 fprintf( fp, "Tree = UPGMA (2).\n" );
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300 else if( treemethod == 'p' )
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301 fprintf( fp, "Tree = UPGMA (1).\n" );
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302 else
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303 fprintf( fp, "Unknown tree.\n" );
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304
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305 if( use_fft )
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306 {
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307 fprintf( fp, "FFT on\n" );
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308 if( scoremtx == -1 )
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309 fprintf( fp, "Basis : 4 nucleotides\n" );
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310 else
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311 {
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312 if( fftscore )
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313 fprintf( fp, "Basis : Polarity and Volume\n" );
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314 else
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315 fprintf( fp, "Basis : 20 amino acids\n" );
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316 }
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317 fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
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318 fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
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319 }
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320 else
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321 fprintf( fp, "FFT off\n" );
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322 fflush( fp );
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323 }
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324
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325
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326 int main( int argc, char *argv[] )
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327 {
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328 static int nlen[M];
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329 static char **name, **seq;
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330 static char **mseq1, **mseq2;
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331 static char **aseq;
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332 static char **bseq;
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333 static double **pscore;
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334 static double **eff;
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335 static double **node0, **node1;
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336 int i, j;
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337 static int ***topol;
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338 static double **len;
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339 FILE *prep;
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340 char c;
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341 int alloclen;
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342
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343 arguments( argc, argv );
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344 getnumlen( stdin );
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345 rewind( stdin );
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346
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347 name = AllocateCharMtx( njob, B+1 );
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348 seq = AllocateCharMtx( njob, nlenmax*5+1 );
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349 aseq = AllocateCharMtx( njob, nlenmax*5+1 );
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350 bseq = AllocateCharMtx( njob, nlenmax*5+1 );
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351 mseq1 = AllocateCharMtx( njob, 0 );
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352 mseq2 = AllocateCharMtx( njob, 0 );
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353 alloclen = nlenmax*5;
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354
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355 topol = AllocateIntCub( njob, 2, njob );
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356 len = AllocateDoubleMtx( njob, 2 );
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357 pscore = AllocateDoubleMtx( njob, njob );
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358 eff = AllocateDoubleMtx( njob, njob );
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359 node0 = AllocateDoubleMtx( njob, njob );
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360 node1 = AllocateDoubleMtx( njob, njob );
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361
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362 #if 0
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363 Read( name, nlen, seq );
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364 #else
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365 readData_pointer( stdin, name, nlen, seq );
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366 #endif
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367
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368 constants( njob, seq );
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369
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370 #if 0
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371 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
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372 #endif
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373
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374 initSignalSM();
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375
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376 initFiles();
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377
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378 WriteOptions( trap_g );
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379
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380 c = seqcheck( seq );
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381 if( c )
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382 {
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383 fprintf( stderr, "Illeagal character %c\n", c );
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384 exit( 1 );
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385 }
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386
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387 writePre( njob, name, nlen, seq, 0 );
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388
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389 if( tbutree == 0 )
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390 {
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391 for( i=1; i<njob; i++ )
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392 {
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393 if( nlen[i] != nlen[0] )
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394 {
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395 fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
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396 exit( 1 );
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397 }
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398 }
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399 for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
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400 {
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401 /*
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402 pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
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403 */
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404 pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
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405 }
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406 }
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407 else
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408 {
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409 fprintf( stderr, "Loading 'hat2' ... " );
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410 prep = fopen( "hat2", "r" );
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411 if( prep == NULL ) ErrorExit( "Make hat2." );
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412 readhat2_pointer( prep, njob, name, pscore );
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413 fclose( prep );
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414 fprintf( stderr, "done.\n" );
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415
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416 #if 0
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417 prep = fopen( "hat2_check", "w" );
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418 WriteHat2( prep, njob, name, pscore );
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419 fclose( prep );
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420 #endif
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421
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422 }
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423
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424 fprintf( stderr, "Constructing dendrogram ... " );
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425 if( treemethod == 'x' )
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426 supg( njob, pscore, topol, len );
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427 else if( treemethod == 's' )
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428 spg( njob, pscore, topol, len );
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429 else if( treemethod == 'p' )
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430 upg2( njob, pscore, topol, len );
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431 else
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432 ErrorExit( "Incorrect tree\n" );
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433 fprintf( stderr, "done.\n" );
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434
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435 countnode( njob, topol, node0 );
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436 if( tbrweight )
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437 {
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438 weight = 3;
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439 utree = 0; counteff( njob, topol, len, eff ); utree = 1;
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440 }
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441 else
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442 {
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443 for( i=0; i<njob; i++ ) eff[i][i] = 1.0;
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444 }
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445
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446
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447 for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
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448
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449 treebase( name, nlen, bseq, aseq, mseq1, mseq2, pscore, topol, len, eff, alloclen );
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450
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451 fprintf( trap_g, "done\n" );
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452 fclose( trap_g );
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453
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454 writePre( njob, name, nlen, aseq, !contin );
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455 writeData_pointer( stdout, njob, name, nlen, aseq );
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456 #if IODEBUG
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457 fprintf( stderr, "OSHIMAI\n" );
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458 #endif
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459 SHOWVERSION;
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460 return( 0 );
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461 }