binaries/src/mafft/core/replaceu.c

   1 #include "mltaln.h"
   2
   3 #define DEBUG 0
   4
   5 static int seedoffset;
   6
   7 static void replace_unusual( int n, char **seq, char *usual, char unknown, int (*uporlow)( int ) )
   8 {
   9         int i;
  10         char *pt;
  11         for( i=0; i<n; i++ )
  12         {
  13                 pt = seq[i];
  14                 while( *pt )
  15                 {
  16                         if( !strchr( usual, *pt ) ) *pt = unknown;
  17                         else *pt = uporlow( *pt );
  18                         pt++;
  19                 }
  20         }
  21 }
  22
  23
  24 void arguments( int argc, char *argv[] )
  25 {
  26     int c;
  27
  28         seedoffset = 0;
  29         inputfile = NULL;
  30
  31     while( --argc > 0 && (*++argv)[0] == '-' )
  32         {
  33         while ( (c = *++argv[0]) )
  34                 {
  35             switch( c )
  36             {
  37                                 case 'o':
  38                                         seedoffset = atoi( *++argv );
  39                                         fprintf( stderr, "seedoffset = %d\n", seedoffset );
  40                                         --argc;
  41                                         goto nextoption;
  42                                 case 'i':
  43                                         inputfile = *++argv;
  44                                         fprintf( stderr, "inputfile = %s\n", inputfile );
  45                                         --argc;
  46                                         goto nextoption;
  47                 default:
  48                     fprintf( stderr, "illegal option %c\n", c );
  49                     argc = 0;
  50                     break;
  51             }
  52                 }
  53                 nextoption:
  54                         ;
  55         }
  56     if( argc != 0 )
  57     {
  58         fprintf( stderr, "options: Check source file !\n" );
  59         exit( 1 );
  60     }
  61 }
  62
  63
  64
  65 int main( int argc, char *argv[] )
  66 {
  67         FILE *infp;
  68         int nlenmin;
  69         char **name;
  70         char **seq;
  71         int *nlen;
  72         int i;
  73         char *usual;
  74
  75         arguments( argc, argv );
  76
  77         if( inputfile )
  78         {
  79                 infp = fopen( inputfile, "r" );
  80                 if( !infp )
  81                 {
  82                         fprintf( stderr, "Cannot open %s\n", inputfile );
  83                         exit( 1 );
  84                 }
  85         }
  86         else
  87                 infp = stdin;
  88
  89
  90         dorp = NOTSPECIFIED;
  91         getnumlen_casepreserve( infp, &nlenmin );
  92
  93         fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
  94
  95         seq = AllocateCharMtx( njob, nlenmax+1 );
  96         name = AllocateCharMtx( njob, B+1 );
  97         nlen = AllocateIntVec( njob );
  98
  99         readData_pointer_casepreserve( infp, name, nlen, seq );
 100
 101 //      for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
 102
 103 #if 0
 104         FILE *origfp;
 105         origfp = fopen( "_original", "w" );
 106         if( !origfp )
 107         {
 108                 fprintf( stderr, "Cannot open _original\n" );
 109                 exit( 1 );
 110         }
 111         for( i=0; i<njob; i++ )
 112         {
 113                 nlen[i] = strlen( seq[i] );
 114                 fprintf( origfp, ">%s\n", name[i]+1 );
 115                 if( seq[i][nlen[i]-1] == '\n' ) seq[i][nlen[i]-1] = 0;
 116                 fprintf( origfp, "%s\n", seq[i] );
 117         }
 118         fclose( origfp );
 119 #endif
 120
 121         if( dorp == 'p' )
 122         {
 123                 usual = "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv-.";
 124                 replace_unusual( njob, seq, usual, 'X', toupper );
 125         }
 126         else
 127         {
 128                 usual = "ATGCUatgcu-";
 129                 replace_unusual( njob, seq, usual, 'n', tolower );
 130         }
 131
 132
 133
 134         for( i=0; i<njob; i++ )
 135         {
 136                 fprintf( stdout, ">%d_oripos_%s\n", i+seedoffset, name[i] );
 137                 fprintf( stdout, "%s\n", seq[i] );
 138         }
 139
 140         free( nlen );
 141         FreeCharMtx( seq );
 142         FreeCharMtx( name );
 143
 144         return( 0 );
 145 }