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##
## Patch to readseq to allow input sequence symbols to be translated
## to different output sequence symbols. This has not been tested,
## as of 22 Dec 94. D.Gilbert
##
diff -bwrc old/Makefile rtrans/Makefile
*** old/Makefile Thu Dec 22 08:58:41 1994
--- rtrans/Makefile Thu Dec 22 08:58:31 1994
***************
*** 13,21 ****
CFLAGS=
#CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
# instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
! DOCS= Readme Readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
# NCBI toolkit support for ASN.1 reader
--- 13,23 ----
CFLAGS=
#CFLAGS= -DSMALLCHECKSUM # if you prefer to use a GCG-standard 13 bit checksum
# instead of a full 32 bit checksum. This may enhance compatibility w/ GCG software
+ #CFLAGS= -DTRANSLATE # if you want option to translate certain input sequence symbols
+ # to a different output sequence symbols
SOURCES= readseq.c ureadseq.c ureadseq.h ureadasn.c
! DOCS= Readme readseq.help Formats Stdfiles Makefile Make.com add.gdemenu *.std
# NCBI toolkit support for ASN.1 reader
diff -bwrc old/readseq.c rtrans/readseq.c
*** old/readseq.c Thu Dec 22 08:58:41 1994
--- rtrans/readseq.c Thu Dec 22 09:01:05 1994
***************
*** 338,343 ****
--- 338,347 ----
fprintf(stderr, " -o[utput=]out.seq redirect Output\n");
fprintf(stderr, " -p[ipe] Pipe (command line, <stdin, >stdout)\n");
fprintf(stderr, " -r[everse] change to Reverse-complement\n");
+ #ifdef TRANSLATE
+ fprintf(stderr, " -t[ranslate=]io translate input symbol [i] to output symbol [o] \n");
+ fprintf(stderr, " use several -tio to translate several symbols \n");
+ #endif
fprintf(stderr, " -v[erbose] Verbose progress\n");
fprintf(stderr, " -f[ormat=]# Format number for output, or\n");
fprintf(stderr, " -f[ormat=]Name Format name for output:\n");
***************
*** 474,479 ****
--- 478,486 ----
foo = NULL;
gPrettyInit(gPretty);
+ #ifdef TRANSLATE
+ gTranslateInit();
+ #endif
}
***************
*** 590,595 ****
--- 597,615 ----
outform = parseformat( sparam);
return kOptOkay;
}
+
+ #ifdef TRANSLATE
+ if (checkopt( false, sopt, "-translate", 3)) {/* -translate=io */
+ if (*sparam==0) { for (sparam= sopt+3; isalpha(*sparam); sparam++) ; }
+ if (*sparam) gTranslate[*sparam]= sparam[1];
+ return kOptOkay;
+ }
+ if (checkopt( false, sopt, "-t", 2)) { /* shorthand is -tio */
+ if (*sparam==0) sparam= sopt+2;
+ if (*sparam) gTranslate[*sparam]= sparam[1];
+ return kOptOkay;
+ }
+ #endif
if (checkopt( false, sopt, "-output", 3)) {/* -output=myseq */
if (*sparam==0) { for (sparam= sopt+3; isalpha(*sparam); sparam++) ; }
diff -bwrc old/ureadseq.c rtrans/ureadseq.c
*** old/ureadseq.c Thu Dec 22 08:58:41 1994
--- rtrans/ureadseq.c Thu Dec 22 09:01:43 1994
***************
*** 162,168 ****
--- 162,172 ----
}
else V->seq = ptr;
}
+ #ifdef TRANSLATE
+ V->seq[(V->seqlen)++] = gTranslate[*s];
+ #else
V->seq[(V->seqlen)++] = *s;
+ #endif
}
s++;
}
diff -bwrc old/ureadseq.h rtrans/ureadseq.h
*** old/ureadseq.h Thu Dec 22 08:58:41 1994
--- rtrans/ureadseq.h Thu Dec 22 08:58:28 1994
***************
*** 113,118 ****
--- 113,126 ----
extern prettyopts gPretty;
#endif
+ #ifdef TRANSLATE
+ #ifdef UREADSEQ_G
+ char gTranslate[256];
+ #else
+ extern char gTranslate[256];
+ #endif
+ #define gTranslateInit() { short c; for(c=0; c<256; c++) gTranslate[c]= c; }
+ #endif
#ifdef __cplusplus
extern "C" {
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