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

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author nick
date Thu, 02 Feb 2017 18:44:31 -0500
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18
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1 #include "mltaln.h"
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2
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3 #define DEBUG 0
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4
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5 char *alignmentfile;
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6
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7 static void fillorichar( int nseq, int *oripos, char **a, char **s )
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8 {
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9 int i;
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10 char *pta, *pts;
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11 for( i=0; i<nseq; i++ )
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12 {
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13 pta = a[i];
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14 pts = s[oripos[i]];
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15 while( *pta )
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16 {
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17 if( *pta != '-' ) *pta = *pts++;
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18 if( *pta++ == 0 )
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19 {
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20 fprintf( stderr, "ERROR!!\n" );
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21 fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
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22 exit( 1 );
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23 }
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24 }
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25 if( *pts != 0 )
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26 {
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27 fprintf( stderr, "ERROR!!\n" );
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28 fprintf( stderr, "alignment is inconsistent with the original sequences\n" );
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29 exit( 1 );
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30 }
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31 }
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32 }
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33
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34 void arguments( int argc, char *argv[] )
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35 {
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36 int c;
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37
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38 while( --argc > 0 && (*++argv)[0] == '-' )
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39 {
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40 while ( (c = *++argv[0]) )
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41 {
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42 switch( c )
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43 {
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44 case 'i':
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45 inputfile = *++argv;
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46 --argc;
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47 goto nextoption;
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48 case 'a':
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49 alignmentfile = *++argv;
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50 --argc;
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51 goto nextoption;
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52 default:
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53 fprintf( stderr, "illegal option %c\n", c );
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54 argc = 0;
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55 break;
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56 }
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57 }
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58 nextoption:
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59 ;
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60 }
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61 if( argc != 0 )
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62 {
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63 fprintf( stderr, "options: Check source file !\n" );
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64 exit( 1 );
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65 }
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66 }
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67
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68
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69
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70 int main( int argc, char *argv[] )
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71 {
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72 FILE *infp;
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73 FILE *alfp;
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74 char **name;
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75 char **aname;
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76 char **oname;
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77 char **seq;
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78 char **aseq;
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79 int *nlen;
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80 int *oripos;
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81 char *npt, *npt0, *npt2, *pt, *pt2;
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82 int i, o, prelen;
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83 int nlenmin;
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84 int njobs, njoba;
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85
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86 arguments( argc, argv );
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87
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88 if( inputfile )
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89 {
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90 infp = fopen( inputfile, "r" );
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91 if( !infp )
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92 {
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93 fprintf( stderr, "Cannot open %s\n", inputfile );
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94 exit( 1 );
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95 }
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96 }
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97 else
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98 infp = stdin;
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99
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100 if( alignmentfile )
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101 {
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102 alfp = fopen( alignmentfile, "r" );
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103 if( !alfp )
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104 {
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105 fprintf( stderr, "Cannot open %s\n", alignmentfile );
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106 exit( 1 );
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107 }
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108 }
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109 else
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110 {
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111 fprintf( stderr, "No alignment is given.\n" );
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112 exit( 1 );
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113 }
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114
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115 dorp = NOTSPECIFIED;
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116 getnumlen_casepreserve( infp, &nlenmin );
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117 njobs = njob;
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118 // fprintf( stderr, "in infp, %d x %d - %d %c\n", njob, nlenmin, nlenmax, dorp );
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119
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120 seq = AllocateCharMtx( njob, nlenmax+1 );
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121 name = AllocateCharMtx( njob, B+1 );
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122 nlen = AllocateIntVec( njob );
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123 oripos = AllocateIntVec( njob );
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124 readData_pointer_casepreserve( infp, name, nlen, seq );
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125
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126 dorp = NOTSPECIFIED;
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127 getnumlen( alfp );
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128 njoba = njob;
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129 // fprintf( stderr, "in alfp, %d x %d %c\n", njob, nlenmax, dorp );
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130 aseq = AllocateCharMtx( njob, nlenmax+1 );
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131 aname = AllocateCharMtx( njob, B+1 );
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132 oname = AllocateCharMtx( njob, B+1 );
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133 readData_pointer( alfp, aname, nlen, aseq );
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134
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135 for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
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136
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137 if( njoba != njobs )
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138 {
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139 fprintf( stderr, "ERROR!!\n" );
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140 fprintf( stderr, "In input file,\n" );
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141 fprintf( stderr, "njob = %d\n", njobs );
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142 fprintf( stderr, "but in alignment file,\n" );
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143 fprintf( stderr, "njob = %d\n", njoba );
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144 exit( 1 );
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145 }
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146
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147 for( i=0; i<njob; i++ )
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148 {
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149 #if 0
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150 if( strstr( aname[i], "_seed_" ) )
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151 {
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152 npt2 = aname[i] + 7;
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153 strcpy( oname[i], "=_seed_" );
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154 }
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155 else
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156 {
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157 npt2 = aname[i] + 1;
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158 strcpy( oname[i], "=" );
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159 }
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160
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161 fprintf( stderr, "npt2 = %s\n", npt2 );
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162
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163 o = oripos[i] = atoi( npt2 );
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164 npt = strstr( npt2, "_oe_" );
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165 if( npt == NULL )
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166 {
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167 fprintf( stderr, "Format error!\n" );
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168 exit( 1 );
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169 }
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170 npt += 4;
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171 strcat( oname[i], npt+1 );
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172 #endif
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173 npt0 = strstr( aname[i], "_os_" );
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174 if( npt0 == NULL )
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175 {
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176 fprintf( stderr, "Format error!\n" );
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177 exit( 1 );
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178 }
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179 npt2 = npt0 + 4;
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180 o = oripos[i] = atoi( npt2 );
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181
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182 npt = strstr( aname[i], "_oe_" );
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183 if( npt == NULL )
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184 {
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185 fprintf( stderr, "Format error!\n" );
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186 exit( 1 );
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187 }
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188 npt += 4;
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189
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190 pt2 = npt;
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191 pt = npt2 - 4;
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192 while( *pt ) *pt++ = *pt2++; // okashii
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193
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194 prelen = npt0-aname[i];
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195 strncpy( oname[i], aname[i], prelen ); oname[i][prelen] = 0;
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196 strcat( oname[i], npt0 );
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197
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198 #if 0
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199 pt = strstr( aname[i], "_numo_e" );
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200 if( pt ) pt += 8;
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201 else pt = aname[i] + 1;
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202
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203 if( strstr( pt, "_seed_" ) ) pt += 6;
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204
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205 fprintf( stderr, "pt = :%s:\n", pt );
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206
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207 #endif
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208 // fprintf( stderr, "npt0 = :%s:\n", npt0 );
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209 //
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210 // reporterr( "oname[i] = %s\n", oname[i] );
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211 // reporterr( "aname[i] = %s\n", aname[i] );
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212 // reporterr( " name[i] = %s\n", name[i] );
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213
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214 // fprintf( stderr, "aname[i] = :%s:\n", aname[i] );
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215 // fprintf( stderr, "pt = :%s:\n", pt );
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216 // fprintf( stderr, "oname[i] = :%s:\n", oname[i] );
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217 // fprintf( stderr, "name[o] = :%s:\n", name[o] );
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218
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219 if( strncmp( npt0, name[o]+1, 10 ) )
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220 {
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221 fprintf( stderr, "ERROR!!\n" );
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222 fprintf( stderr, "In input file,\n" );
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223 fprintf( stderr, "name[%d] = %s\n", o, name[o] );
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224 fprintf( stderr, "but in alignment file,\n" );
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225 fprintf( stderr, "oname[%d] = %s\n", i, oname[i] );
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226 fprintf( stderr, "npt0 = %s\n", npt0 );
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227 fprintf( stderr, "prelen = %d\n", prelen );
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228 fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
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229 exit( 1 );
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230 }
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231 #if 0
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232 else
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233 {
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234 fprintf( stderr, "OK!!\n" );
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235 fprintf( stderr, "In input file,\n" );
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236 fprintf( stderr, "name[%d] = %s\n", o, name[o] );
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237 fprintf( stderr, "and in alignment file,\n" );
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238 fprintf( stderr, "name[%d] = %s\n", i, aname[i] );
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239 fprintf( stderr, "\n" );
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240 }
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241 #endif
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242 }
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243 // fprintf( stderr, "seq[0] = %s\n", seq[0] );
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244 // fprintf( stderr, "aseq[0] = %s\n", aseq[0] );
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245
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246 fillorichar( njob, oripos, aseq, seq );
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247
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248
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249 writeData_pointer( stdout, njob, oname, nlen, aseq );
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250
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251 FreeCharMtx( seq );
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252 FreeCharMtx( aseq );
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253 FreeCharMtx( name );
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254 FreeCharMtx( aname );
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255 FreeCharMtx( oname );
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256 free( nlen );
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257 free( oripos );
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258
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259 return( 0 );
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260 }