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annotate mafft/core/multi2hat3s.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
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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 #define TSUYOSAFACTOR 100
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7
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8
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9 static int nhomologs;
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10 static int seedoffset;
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11
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12 void strip( char *s )
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13 {
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14 char *pt = s;
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15 while( *++pt )
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16 if( *pt == '\n' ) *pt = 0;
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17 }
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18
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19
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20 void arguments( int argc, char *argv[] )
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21 {
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22 int c;
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23
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24 seedoffset = 0;
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25 nhomologs = 1;
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26 inputfile = NULL;
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27 fftkeika = 0;
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28 pslocal = -1000.0;
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29 constraint = 0;
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30 nblosum = 62;
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31 fmodel = 0;
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32 calledByXced = 0;
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33 devide = 0;
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34 use_fft = 0;
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35 fftscore = 1;
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36 fftRepeatStop = 0;
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37 fftNoAnchStop = 0;
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38 weight = 3;
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39 utree = 1;
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40 tbutree = 1;
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41 refine = 0;
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42 check = 1;
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43 cut = 0.0;
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44 disp = 0;
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45 outgap = 1;
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46 alg = 'A';
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47 mix = 0;
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48 tbitr = 0;
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49 scmtd = 5;
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50 tbweight = 0;
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51 tbrweight = 3;
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52 checkC = 0;
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53 treemethod = 'x';
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54 contin = 0;
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55 scoremtx = 1;
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56 kobetsubunkatsu = 0;
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57 divpairscore = 0;
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58 dorp = NOTSPECIFIED;
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59 ppenalty = NOTSPECIFIED;
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60 ppenalty_OP = NOTSPECIFIED;
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61 ppenalty_ex = NOTSPECIFIED;
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62 ppenalty_EX = NOTSPECIFIED;
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63 poffset = NOTSPECIFIED;
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64 kimuraR = NOTSPECIFIED;
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65 pamN = NOTSPECIFIED;
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66 geta2 = GETA2;
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67 fftWinSize = NOTSPECIFIED;
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68 fftThreshold = NOTSPECIFIED;
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69
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70 while( --argc > 0 && (*++argv)[0] == '-' )
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71 {
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72 while ( ( c = *++argv[0] ) )
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73 {
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74 switch( c )
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75 {
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76 case 'i':
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77 inputfile = *++argv;
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78 fprintf( stderr, "seed = %s\n", inputfile );
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79 --argc;
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80 goto nextoption;
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81 case 't':
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82 nhomologs = myatoi( *++argv );
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83 fprintf( stderr, "nhomologs = %d\n", nhomologs );
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84 --argc;
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85 goto nextoption;
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86 case 'o':
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87 seedoffset = myatoi( *++argv );
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88 fprintf( stderr, "seedoffset = %d\n", seedoffset );
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89 --argc;
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90 goto nextoption;
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91 case 'D':
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92 dorp = 'd';
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93 break;
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94 case 'P':
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95 dorp = 'p';
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96 break;
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97 default:
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98 fprintf( stderr, "illegal option %c\n", c );
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99 argc = 0;
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100 break;
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101 }
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102 }
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103 nextoption:
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104 ;
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105 }
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106 if( argc == 1 )
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107 {
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108 cut = atof( (*argv) );
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109 argc--;
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110 }
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111 if( argc != 0 )
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112 {
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113 fprintf( stderr, "options: Check source file !\n" );
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114 exit( 1 );
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115 }
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116 if( tbitr == 1 && outgap == 0 )
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117 {
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118 fprintf( stderr, "conflicting options : o, m or u\n" );
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119 exit( 1 );
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120 }
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121 if( alg == 'C' && outgap == 0 )
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122 {
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123 fprintf( stderr, "conflicting options : C, o\n" );
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124 exit( 1 );
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125 }
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126 }
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127
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128 int countamino( char *s, int end )
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129 {
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130 int val = 0;
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131 while( end-- )
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132 if( *s++ != '-' ) val++;
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133 return( val );
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134 }
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135
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136 static void pairalign( char **name, int nlen[M], char **seq, double *effarr, int alloclen )
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137 {
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138 int i, j;
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139 FILE *hat3p;
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140 float pscore = 0.0; // by D.Mathog
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141 static double *effarr1 = NULL;
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142 static double *effarr2 = NULL;
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143 char *aseq;
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144 static char **pseq;
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145 LocalHom **localhomtable, *tmpptr;
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146 double tsuyosa;
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147
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148 if( nhomologs < 1 ) nhomologs = 1; // tsuyosa=0.0 wo sakeru
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149 tsuyosa = (double)nhomologs * nhomologs * TSUYOSAFACTOR;
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150 fprintf( stderr, "tsuyosa = %f\n", tsuyosa );
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151 localhomtable = (LocalHom **)calloc( njob, sizeof( LocalHom *) );
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152 for( i=0; i<njob; i++)
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153 {
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154 localhomtable[i] = (LocalHom *)calloc( njob, sizeof( LocalHom ) );
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155 for( j=0; j<njob; j++)
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156 {
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157 localhomtable[i][j].start1 = -1;
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158 localhomtable[i][j].end1 = -1;
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159 localhomtable[i][j].start2 = -1;
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160 localhomtable[i][j].end2 = -1;
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161 localhomtable[i][j].opt = -1.0;
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162 localhomtable[i][j].next = NULL;
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163 }
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164 }
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165
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166 if( effarr1 == NULL )
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167 {
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168 effarr1 = AllocateDoubleVec( njob );
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169 effarr2 = AllocateDoubleVec( njob );
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170 pseq = AllocateCharMtx( 2, 0 );
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171 aseq = AllocateCharVec( nlenmax*9+1 );
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172 #if 0
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173 #else
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174 #endif
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175 }
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176
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177 #if 0
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178 fprintf( stderr, "##### fftwinsize = %d, fftthreshold = %d\n", fftWinSize, fftThreshold );
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179 #endif
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180
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181 #if 0
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182 for( i=0; i<njob; i++ )
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183 fprintf( stderr, "TBFAST effarr[%d] = %f\n", i, effarr[i] );
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184 #endif
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185
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186
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187 // writePre( njob, name, nlen, aseq, 0 );
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188
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189 hat3p = fopen( "hat3", "w" );
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190 if( !hat3p ) ErrorExit( "Cannot open hat3." );
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191 fprintf( stderr, "\n" );
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192 for( i=0; i<njob-1; i++ )
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193 {
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194 for( j=i+1; j<njob; j++ )
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195 {
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196 pseq[0] = seq[i];
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197 pseq[1] = seq[j];
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198
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199 if( strlen( pseq[0] ) != strlen( pseq[1] ) )
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200 {
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201 fprintf( stderr, "## ERROR ###\n" );
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202 fprintf( stderr, "Not aligned, %s - %s\n", name[i], name[j] );
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203 fprintf( stderr, "## ERROR ###\n" );
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204 exit( 1 );
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205 }
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206
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207
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208 fprintf( stderr, "adding %d-%d\r", i, j );
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209 putlocalhom2( pseq[0], pseq[1], localhomtable[i]+j, 0, 0, (int)pscore, strlen( pseq[0] ) );
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210 for( tmpptr=localhomtable[i]+j; tmpptr; tmpptr=tmpptr->next )
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211 {
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212 if( tmpptr->opt == -1.0 ) continue;
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213 if( tmpptr->start1 == -1 ) continue;
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214 fprintf( hat3p, "%d %d %d %6.3f %d %d %d %d k\n", i+seedoffset, j+seedoffset, tmpptr->overlapaa, tmpptr->opt * tsuyosa, tmpptr->start1, tmpptr->end1, tmpptr->start2, tmpptr->end2 );
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215 }
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216 }
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217 }
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218 fprintf( stderr, "\n" );
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219 fclose( hat3p );
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220
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221 #if DEBUG
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222 fprintf( stderr, "calling FreeLocalHomTable\n" );
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223 #endif
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224 FreeLocalHomTable( localhomtable, njob );
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225 #if DEBUG
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226 fprintf( stderr, "done. FreeLocalHomTable\n" );
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227 #endif
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228 }
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229
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230 static void WriteOptions( FILE *fp )
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231 {
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232
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233 if( dorp == 'd' ) fprintf( fp, "DNA\n" );
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234 else
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235 {
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236 if ( scoremtx == 0 ) fprintf( fp, "JTT %dPAM\n", pamN );
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237 else if( scoremtx == 1 ) fprintf( fp, "BLOSUM %d\n", nblosum );
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238 else if( scoremtx == 2 ) fprintf( fp, "M-Y\n" );
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239 }
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240 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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241 if( use_fft ) fprintf( fp, "FFT on\n" );
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242
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243 fprintf( fp, "tree-base method\n" );
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244 if( tbrweight == 0 ) fprintf( fp, "unweighted\n" );
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245 else if( tbrweight == 3 ) fprintf( fp, "clustalw-like weighting\n" );
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246 if( tbitr || tbweight )
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247 {
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248 fprintf( fp, "iterate at each step\n" );
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249 if( tbitr && tbrweight == 0 ) fprintf( fp, " unweighted\n" );
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250 if( tbitr && tbrweight == 3 ) fprintf( fp, " reversely weighted\n" );
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251 if( tbweight ) fprintf( fp, " weighted\n" );
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252 fprintf( fp, "\n" );
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253 }
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254
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255 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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256
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257 if( alg == 'a' )
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258 fprintf( fp, "Algorithm A\n" );
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259 else if( alg == 'A' )
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260 fprintf( fp, "Algorithm A+\n" );
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261 else if( alg == 'S' )
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262 fprintf( fp, "Apgorithm S\n" );
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263 else if( alg == 'C' )
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264 fprintf( fp, "Apgorithm A+/C\n" );
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265 else
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266 fprintf( fp, "Unknown algorithm\n" );
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267
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268 if( treemethod == 'x' )
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269 fprintf( fp, "Tree = UPGMA (3).\n" );
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270 else if( treemethod == 's' )
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271 fprintf( fp, "Tree = UPGMA (2).\n" );
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272 else if( treemethod == 'p' )
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273 fprintf( fp, "Tree = UPGMA (1).\n" );
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274 else
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275 fprintf( fp, "Unknown tree.\n" );
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276
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277 if( use_fft )
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278 {
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279 fprintf( fp, "FFT on\n" );
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280 if( dorp == 'd' )
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281 fprintf( fp, "Basis : 4 nucleotides\n" );
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282 else
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283 {
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284 if( fftscore )
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285 fprintf( fp, "Basis : Polarity and Volume\n" );
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286 else
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287 fprintf( fp, "Basis : 20 amino acids\n" );
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288 }
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289 fprintf( fp, "Threshold of anchors = %d%%\n", fftThreshold );
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290 fprintf( fp, "window size of anchors = %dsites\n", fftWinSize );
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291 }
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292 else
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293 fprintf( fp, "FFT off\n" );
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294 fflush( fp );
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295 }
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296
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297
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298 int main( int argc, char *argv[] )
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299 {
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300 static int nlen[M];
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301 static char **name, **seq;
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302 static char **bseq;
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303 static double *eff;
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304 int i;
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305 char c;
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306 int alloclen;
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307 FILE *infp;
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308
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309 arguments( argc, argv );
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310
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311 if( inputfile )
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312 {
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313 infp = fopen( inputfile, "r" );
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314 if( !infp )
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315 {
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316 fprintf( stderr, "Cannot open %s\n", inputfile );
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317 exit( 1 );
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318 }
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319 }
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320 else
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321 infp = stdin;
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322
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323 getnumlen( infp );
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324 rewind( infp );
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325
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326 if( njob < 2 )
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327 {
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328 fprintf( stderr, "At least 2 sequences should be input!\n"
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329 "Only %d sequence found.\n", njob );
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330 exit( 1 );
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331 }
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332
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333 name = AllocateCharMtx( njob, B+1 );
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334 seq = AllocateCharMtx( njob, nlenmax*9+1 );
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335 bseq = AllocateCharMtx( njob, nlenmax*9+1 );
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336 alloclen = nlenmax*9;
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337
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338 eff = AllocateDoubleVec( njob );
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339
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340 #if 0
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341 Read( name, nlen, seq );
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342 #else
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343 readData_pointer( infp, name, nlen, seq );
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344 #endif
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345 fclose( infp );
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346
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347 constants( njob, seq );
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348
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349 #if 0
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350 fprintf( stderr, "params = %d, %d, %d\n", penalty, penalty_ex, offset );
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351 #endif
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352
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353 initSignalSM();
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354
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355 initFiles();
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356
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357 WriteOptions( trap_g );
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358
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359 c = seqcheck( seq );
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360 if( c )
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361 {
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362 fprintf( stderr, "Illeagal character %c\n", c );
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363 exit( 1 );
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364 }
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365
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366 // writePre( njob, name, nlen, seq, 0 );
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367
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368 for( i=0; i<njob; i++ ) eff[i] = 1.0;
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369
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370
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371 for( i=0; i<njob; i++ ) gappick0( bseq[i], seq[i] );
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372
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373
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374 // for( i=0; i<njob; i++ ) fprintf( stdout, ">_seed_%s\n%s\n", name[i]+1, bseq[i] ); // CHUUI!!
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375 for( i=0; i<njob; i++ ) fprintf( stdout, ">_seed_%s\n%s\n", name[i]+1, seq[i] );
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376
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377 pairalign( name, nlen, seq, eff, alloclen );
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378
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379 fprintf( trap_g, "done.\n" );
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380 #if DEBUG
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381 fprintf( stderr, "closing trap_g\n" );
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382 #endif
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383 fclose( trap_g );
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384
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385 #if IODEBUG
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386 fprintf( stderr, "OSHIMAI\n" );
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387 #endif
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388 SHOWVERSION;
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389 return( 0 );
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390 }