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#include "mltaln.h"
#define DEBUG 0
static int seedoffset;
static void replace_unusual( int n, char **seq, char *usual, char unknown, int (*uporlow)( int ) )
{
int i;
char *pt;
for( i=0; i<n; i++ )
{
pt = seq[i];
while( *pt )
{
if( !strchr( usual, *pt ) ) *pt = unknown;
else *pt = uporlow( *pt );
pt++;
}
}
}
void arguments( int argc, char *argv[] )
{
int c;
seedoffset = 0;
inputfile = NULL;
dorp = NOTSPECIFIED;
while( --argc > 0 && (*++argv)[0] == '-' )
{
while ( (c = *++argv[0]) )
{
switch( c )
{
case 'o':
seedoffset = myatoi( *++argv );
fprintf( stderr, "seedoffset = %d\n", seedoffset );
--argc;
goto nextoption;
case 'i':
inputfile = *++argv;
fprintf( stderr, "inputfile = %s\n", inputfile );
--argc;
goto nextoption;
case 'D':
dorp = 'd';
break;
case 'P':
dorp = 'p';
break;
default:
fprintf( stderr, "illegal option %c\n", c );
argc = 0;
break;
}
}
nextoption:
;
}
if( argc != 0 )
{
fprintf( stderr, "options: Check source file !\n" );
exit( 1 );
}
}
int main( int argc, char *argv[] )
{
FILE *infp;
int nlenmin;
char **name;
char **seq;
int *nlen;
int i;
char *usual;
arguments( argc, argv );
if( inputfile )
{
infp = fopen( inputfile, "r" );
if( !infp )
{
fprintf( stderr, "Cannot open %s\n", inputfile );
exit( 1 );
}
}
else
infp = stdin;
// dorp = NOTSPECIFIED;
getnumlen_casepreserve( infp, &nlenmin );
fprintf( stderr, "%d x %d - %d %c\n", njob, nlenmax, nlenmin, dorp );
seq = AllocateCharMtx( njob, nlenmax+1 );
name = AllocateCharMtx( njob, B+1 );
nlen = AllocateIntVec( njob );
readData_pointer_casepreserve( infp, name, nlen, seq );
fclose( infp );
// for( i=0; i<njob; i++ ) gappick_samestring( seq[i] );
#if 0
FILE *origfp;
origfp = fopen( "_original", "w" );
if( !origfp )
{
fprintf( stderr, "Cannot open _original\n" );
exit( 1 );
}
for( i=0; i<njob; i++ )
{
nlen[i] = strlen( seq[i] );
fprintf( origfp, ">%s\n", name[i]+1 );
if( seq[i][nlen[i]-1] == '\n' ) seq[i][nlen[i]-1] = 0;
fprintf( origfp, "%s\n", seq[i] );
}
fclose( origfp );
#endif
if( dorp == 'p' )
{
usual = "ARNDCQEGHILKMFPSTWYVarndcqeghilkmfpstwyv-.";
replace_unusual( njob, seq, usual, 'X', toupper );
}
else
{
usual = "ATGCUatgcuBDHKMNRSVWYXbdhkmnrsvwyx-";
replace_unusual( njob, seq, usual, 'n', tolower );
}
for( i=0; i<njob; i++ )
{
fprintf( stdout, ">_os_%d_oe_%s\n", i+seedoffset, name[i]+1 );
fprintf( stdout, "%s\n", seq[i] );
}
free( nlen );
FreeCharMtx( seq );
FreeCharMtx( name );
return( 0 );
}
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