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annotate mafft/core/setcore.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 #define SCOREOUT 1
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6
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7 double corethr;
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8 int coreext;
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9
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10 void arguments( int argc, char *argv[] )
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11 {
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12 int c;
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13
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14 fftkeika = 1;
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15 constraint = 0;
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16 nblosum = 62;
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17 fmodel = 0;
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18 calledByXced = 0;
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19 devide = 0;
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20 use_fft = 0;
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21 fftscore = 1;
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22 fftRepeatStop = 0;
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23 fftNoAnchStop = 0;
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24 weight = 3;
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25 utree = 1;
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26 tbutree = 1;
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27 refine = 0;
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28 check = 1;
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29 cut = 0.0;
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30 disp = 0;
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31 outgap = 1;
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32 alg = 'A';
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33 mix = 0;
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34 tbitr = 0;
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35 scmtd = 5;
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36 tbweight = 0;
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37 tbrweight = 3;
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38 checkC = 0;
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39 treemethod = 'x';
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40 contin = 0;
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41 scoremtx = 0;
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42 kobetsubunkatsu = 0;
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43 dorp = NOTSPECIFIED;
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44 ppenalty = NOTSPECIFIED;
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45 ppenalty_ex = NOTSPECIFIED;
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46 poffset = NOTSPECIFIED;
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47 kimuraR = NOTSPECIFIED;
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48 pamN = NOTSPECIFIED;
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49 geta2 = GETA2;
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50 fftWinSize = NOTSPECIFIED;
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51 fftThreshold = NOTSPECIFIED;
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52 corethr = .5;
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53 coreext = 0;
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54
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55 while( --argc > 0 && (*++argv)[0] == '-' )
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56 {
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57 while ( ( c = *++argv[0] ) )
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58 {
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59 switch( c )
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60 {
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61 case 'f':
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62 ppenalty = (int)( atof( *++argv ) * 1000 - 0.5 );
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63 fprintf( stderr, "ppenalty = %d\n", ppenalty );
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64 --argc;
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65 goto nextoption;
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66 case 'g':
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67 ppenalty_ex = (int)( atof( *++argv ) * 1000 - 0.5 );
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68 fprintf( stderr, "ppenalty_ex = %d\n", ppenalty_ex );
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69 --argc;
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70 goto nextoption;
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71 case 'h':
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72 poffset = (int)( atof( *++argv ) * 1000 - 0.5 );
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73 fprintf( stderr, "poffset = %d\n", poffset );
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74 --argc;
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75 goto nextoption;
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76 case 'k':
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77 kimuraR = myatoi( *++argv );
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78 fprintf( stderr, "kimuraR = %d\n", kimuraR );
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79 --argc;
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80 goto nextoption;
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81 case 'b':
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82 nblosum = myatoi( *++argv );
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83 scoremtx = 1;
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84 fprintf( stderr, "blosum %d\n", nblosum );
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85 --argc;
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86 goto nextoption;
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87 case 'j':
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88 pamN = myatoi( *++argv );
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89 scoremtx = 0;
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90 fprintf( stderr, "jtt %d\n", pamN );
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91 --argc;
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92 goto nextoption;
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93 case 'l':
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94 fastathreshold = atof( *++argv );
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95 constraint = 2;
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96 fprintf( stderr, "weighti = %f\n", fastathreshold );
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97 --argc;
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98 goto nextoption;
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99 case 'i':
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100 corethr = atof( *++argv );
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101 fprintf( stderr, "corethr = %f\n", corethr );
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102 --argc;
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103 goto nextoption;
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104 case 'm':
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105 fmodel = 1;
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106 break;
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107 case 'c':
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108 coreext = 1;
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109 break;
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110 case 'r':
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111 fmodel = -1;
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112 break;
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113 case 'D':
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114 dorp = 'd';
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115 break;
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116 case 'P':
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117 dorp = 'p';
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118 break;
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119 case 'e':
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120 fftscore = 0;
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121 break;
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122 case 'O':
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123 fftNoAnchStop = 1;
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124 break;
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diff changeset
125 case 'R':
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126 fftRepeatStop = 1;
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127 break;
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128 case 'Q':
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129 calledByXced = 1;
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130 break;
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131 case 's':
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132 treemethod = 's';
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133 break;
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134 case 'x':
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135 treemethod = 'x';
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136 break;
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137 case 'p':
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138 treemethod = 'p';
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139 break;
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140 case 'a':
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141 alg = 'a';
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142 break;
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143 case 'A':
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144 alg = 'A';
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145 break;
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146 case 'S':
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147 alg = 'S';
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148 break;
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149 case 'C':
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150 alg = 'C';
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151 break;
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152 case 'F':
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153 use_fft = 1;
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154 break;
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155 case 'v':
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156 tbrweight = 3;
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157 break;
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158 case 'd':
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159 disp = 1;
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160 break;
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161 case 'o':
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162 outgap = 0;
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163 break;
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164 /* Modified 01/08/27, default: user tree */
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165 case 'J':
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166 tbutree = 0;
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167 break;
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168 /* modification end. */
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169 case 'z':
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170 fftThreshold = myatoi( *++argv );
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171 --argc;
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172 goto nextoption;
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173 case 'w':
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174 fftWinSize = myatoi( *++argv );
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175 --argc;
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176 goto nextoption;
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177 case 'Z':
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178 checkC = 1;
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179 break;
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180 default:
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181 fprintf( stderr, "illegal option %c\n", c );
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182 argc = 0;
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183 break;
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184 }
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185 }
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186 nextoption:
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187 ;
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188 }
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189 if( argc == 1 )
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190 {
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191 cut = atof( (*argv) );
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192 argc--;
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193 }
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194 if( argc != 0 )
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195 {
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196 fprintf( stderr, "options: Check source file !\n" );
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197 exit( 1 );
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198 }
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199 if( tbitr == 1 && outgap == 0 )
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200 {
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201 fprintf( stderr, "conflicting options : o, m or u\n" );
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202 exit( 1 );
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parents:
diff changeset
203 }
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204 if( alg == 'C' && outgap == 0 )
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diff changeset
205 {
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206 fprintf( stderr, "conflicting options : C, o\n" );
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207 exit( 1 );
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diff changeset
208 }
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diff changeset
209 }
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diff changeset
210
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211
e4d75f9efb90 planemo upload commit b'4303231da9e48b2719b4429a29b72421d24310f4\n'-dirty
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212
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213 static void WriteOptions( FILE *fp )
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214 {
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215
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216 if( dorp == 'd' ) fprintf( fp, "DNA\n" );
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217 else
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218 {
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219 if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
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220 else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
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221 else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
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222 }
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223 fprintf( stderr, "Gap Penalty = %+5.2f, %+5.2f, %+5.2f\n", (double)ppenalty/1000, (double)ppenalty_ex/1000, (double)poffset/1000 );
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224 if( use_fft ) fprintf( fp, "FFT on\n" );
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225
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226 fprintf( fp, "tree-base method\n" );
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227 if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
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228 else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
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229 if( tbitr || tbweight )
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230 {
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231 fprintf( fp, "iterate at each step\n" );
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232 if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
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233 if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
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234 if( tbweight ) fprintf( fp, " weighted\n" );
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235 fprintf( fp, "\n" );
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diff changeset
236 }
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237
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238 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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239
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240 if( alg == 'a' )
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241 fprintf( fp, "Algorithm A\n" );
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242 else if( alg == 'A' )
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243 fprintf( fp, "Algorithm A+\n" );
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244 else if( alg == 'S' )
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245 fprintf( fp, "Apgorithm S\n" );
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246 else if( alg == 'C' )
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247 fprintf( fp, "Apgorithm A+/C\n" );
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248 else
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249 fprintf( fp, "Unknown algorithm\n" );
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250
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251 if( treemethod == 'x' )
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252 fprintf( fp, "Tree = UPGMA (3).\n" );
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253 else if( treemethod == 's' )
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254 fprintf( fp, "Tree = UPGMA (2).\n" );
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255 else if( treemethod == 'p' )
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256 fprintf( fp, "Tree = UPGMA (1).\n" );
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257 else
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258 fprintf( fp, "Unknown tree.\n" );
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259
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260 if( use_fft )
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261 {
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262 fprintf( fp, "FFT on\n" );
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263 if( dorp == 'd' )
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264 fprintf( fp, "Basis : 4 nucleotides\n" );
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265 else
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266 {
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267 if( fftscore )
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268 fprintf( fp, "Basis : Polarity and Volume\n" );
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269 else
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270 fprintf( fp, "Basis : 20 amino acids\n" );
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271 }
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272 fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
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273 fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
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274 }
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275 else
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276 fprintf( fp, "FFT off\n" );
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277 fflush( fp );
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278 }
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279
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280
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281 int main( int argc, char *argv[] )
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282 {
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283 static int nlen[M];
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284 static char **name, **seq;
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285 static char **oseq;
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286 static double **pscore;
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287 static double *eff;
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288 static double **node0, **node1;
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289 static double *gapc;
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290 static double *avgap;
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291 double tmpavgap;
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292 int i, j, m, goffset;
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293 static int ***topol;
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294 static double **len;
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295 FILE *prep;
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296 char c;
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297 int corestart, coreend;
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298 int alloclen;
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299 int winsize;
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300 char *pt, *ot;
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301 double gapmin;
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302
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303 arguments( argc, argv );
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304
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305 getnumlen( stdin );
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306 rewind( stdin );
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307
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308 if( njob < 2 )
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309 {
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310 fprintf( stderr, "At least 2 sequences should be input!\n"
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311 "Only %d sequence found.\n", njob );
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312 exit( 1 );
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313 }
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314
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315 seq = AllocateCharMtx( njob, nlenmax*9+1 );
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316 name = AllocateCharMtx( njob, B+1 );
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317 oseq = AllocateCharMtx( njob, nlenmax*9+1 );
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318 alloclen = nlenmax*9;
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319
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320 topol = AllocateIntCub( njob, 2, njob );
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321 len = AllocateDoubleMtx( njob, 2 );
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322 pscore = AllocateDoubleMtx( njob, njob );
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323 eff = AllocateDoubleVec( njob );
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324 node0 = AllocateDoubleMtx( njob, njob );
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325 node1 = AllocateDoubleMtx( njob, njob );
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326 gapc = AllocateDoubleVec( alloclen );
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327 avgap = AllocateDoubleVec( alloclen );
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328
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329 #if 0
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330 Read( name, nlen, seq );
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331 #else
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332 readData_pointer( stdin, name, nlen, seq );
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333 #endif
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334
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335 constants( njob, seq );
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336
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337 #if 0
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338 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
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339 #endif
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340
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341 initSignalSM();
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342
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343 initFiles();
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344
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345 WriteOptions( trap_g );
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346
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347 c = seqcheck( seq );
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348 if( c )
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349 {
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350 fprintf( stderr, "Illeagal character %c\n", c );
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351 exit( 1 );
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352 }
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353
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354 writePre( njob, name, nlen, seq, 0 );
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355
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356 if( tbutree == 0 )
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357 {
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358 for( i=1; i<njob; i++ )
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359 {
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360 if( nlen[i] != nlen[0] )
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361 {
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362 fprintf( stderr, "Input pre-aligned seqences or make hat2.\n" );
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363 exit( 1 );
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364 }
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365 }
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366 for( i=0; i<njob-1; i++ ) for( j=i+1; j<njob; j++ )
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367 {
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368 /*
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369 pscore[i][j] = (double)score_calc1( seq[i], seq[j] );
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370 */
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371 pscore[i][j] = (double)substitution_hosei( seq[i], seq[j] );
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372 }
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373 }
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374 else
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375 {
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376 fprintf( stderr, "Loading 'hat2' ... " );
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377 prep = fopen( "hat2", "r" );
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378 if( prep == NULL ) ErrorExit( "Make hat2." );
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379 readhat2_pointer( prep, njob, name, pscore );
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380 fclose( prep );
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381 fprintf( stderr, "done.\n" );
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382
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383 #if 0
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384 prep = fopen( "hat2_check", "w" );
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385 WriteHat2( prep, njob, name, pscore );
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386 fclose( prep );
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387 #endif
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388
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389 }
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390
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391 fprintf( stderr, "Constructing dendrogram ... " );
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392 if( treemethod == 'x' )
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393 supg( njob, pscore, topol, len );
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394 else if( treemethod == 's' )
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395 spg( njob, pscore, topol, len );
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396 else if( treemethod == 'p' )
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397 upg2( njob, pscore, topol, len );
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398 else
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399 ErrorExit( "Incorrect tree\n" );
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400 fprintf( stderr, "done.\n" );
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401
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402 countnode( njob, topol, node0 );
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403 if( tbrweight )
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404 {
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405 weight = 3;
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406 #if 0
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407 utree = 0; counteff( njob, topol, len, eff ); utree = 1;
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408 #else
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409 counteff_simple( njob, topol, len, eff );
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410 #endif
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411 }
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412 else
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413 {
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414 for( i=0; i<njob; i++ ) eff[i] = 1.0;
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415 }
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416
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417
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418 for( i=0; i<nlenmax; i++ )
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419 {
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420 gapc[i] = 0.0;
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421 for( j=0; j<njob; j++ )
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422 {
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423 if( seq[j][i] == '-' ) gapc[i] += eff[j];
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424 }
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425 }
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426
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427 gapmin = 1.0;
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428 winsize = fftWinSize;
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429 goffset = winsize/2;
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430 tmpavgap = 0.0;
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431 corestart = coreend = -1;
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432 for( i=0; i<winsize; i++ )
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433 {
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434 tmpavgap += gapc[i];
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435 }
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436 for( i=winsize; i<nlenmax; i++ )
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437 {
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438 m = i - goffset;
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439 avgap[m] = tmpavgap / winsize;
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440 // fprintf( stdout, "%d %f %f\n", m, avgap[m], gapc[i] );
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441 if( avgap[m] < corethr )
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442 {
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443 if( corestart == -1 )
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444 corestart = i - winsize;
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445 // fprintf( stdout, "ok, gapmin = %f, corestart = %d, coreend = %d\n", gapmin, corestart, coreend );
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446 if( avgap[m] < gapmin )
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447 {
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448 gapmin = avgap[m];
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449 }
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450 coreend = i;
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451 }
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452 tmpavgap -= gapc[i-winsize];
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453 tmpavgap += gapc[i];
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454 }
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455 if( corestart == -1 || coreend == -1 )
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456 {
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457 corestart = 0;
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458 coreend = nlenmax-1;
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459 }
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460
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461 for( i=0; i<njob; i++ )
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462 {
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463 pt = oseq[i];
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464 m = winsize;
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465 while( m-- ) *pt++ = '-';
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466 for( j=corestart; j<=coreend; j++ )
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467 *pt++ = seq[i][j];
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468 m = winsize;
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469 while( m-- ) *pt++ = '-';
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470 *pt = 0;
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471
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472 ot = oseq[i]+winsize-1;
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473 pt = seq[i]+corestart-1;
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474 if( coreext ) m = winsize;
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475 else m = 0;
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476 while( m && --pt > seq[i] )
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477 if( *pt != '-' )
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478 {
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479 *ot-- = *pt;
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480 m--;
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481 }
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482
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483 ot = oseq[i]+winsize+coreend-corestart+1;
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484 pt = seq[i]+coreend;
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485 if( coreext ) m = winsize;
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486 else m = 0;
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487 while( m && *(++pt) )
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488 {
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489 if( *pt != '-' )
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490 {
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491 *ot++ = *pt;
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492 m--;
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493 }
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494 }
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495 fprintf( stdout, ">%s\n", name[i] );
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496 fprintf( stdout, "%s\n", oseq[i] );
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497 }
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498
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499 exit( 1 );
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500
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501 SHOWVERSION;
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502 return( 0 );
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503 }