PRIMER (VMS)
Christoph Gartmann
GARTMANN at IMMUNBIO.MPG.DE
Fri Jan 28 16:42:00 EST 1994
In <2ib1mb$hi9 at hermod.uio.no> rodrigol at biomaster.uio.no writes:
> Please port all relevant fixes as I'm sure a lot of people are
> interested. Since support for the program is not exsistant and
> 'potential' updates are not available, the user community is left
> to it's own mercy and that of people like you and Liz.
I hope that the rest is self explaining. The version here is V0.5, is
there a newer one?
************
File DISK11:[PRIMER]TEXT.C;1
116
/* Program exits if no sample sequence file name given - Liz Cowe, Sept 93 */
/* gets(line); while(line[0] == '\0' || line[0] == '\n') gets(line); */
/* sscanf(line,"%s",sequence_file_name); */
gets(line);
if(sscanf(line,"%s",sequence_file_name) != 1 ) { exit(1); }
if((fp = fopen(sequence_file_name,"r")) == NULL) {
printf("*** error: can't open %s\n",sequence_file_name); test1 = 1;
124
******
File DISK11:[PRIMER]TEXT.C_ORIGINAL;1
116
gets(line); while(line[0] == '\0' || line[0] == '\n') gets(line);
sscanf(line,"%s",sequence_file_name);
if((fp = fopen(sequence_file_name,"r")) == NULL) {
printf("*** error: can't open %s\n",sequence_file_name); test1 = 1;
119
************
************
File DISK11:[PRIMER]TEXT.C;1
1380
/* Was returning 0 if accepted default for num_terminators - Liz Cowe, Sep 93 */
/* line[0] = '\0'; gets(line); i = 0; num = 0; */
/* n = sscanf(line,"%d",&num); */
/* if(n <= 0) num = 0; */
/* else if(num > 3) { printf("***clamping for 3 bases\n"); num = 3; */
line[0] = '\0'; gets(line);
if(sscanf(line,"%d",&num) == 1) { num_terminators = num; }
if(num_terminators > 3) { printf("***clamping for 3 bases\n");
num_terminators = 3; }
if(num_terminators == 1) { strcpy(terminator[0],"C");
strcpy(terminator[1],"G"); strcpy(terminator[2],""); }
else if(num_terminators == 2) { strcpy(terminator[0],"CC");
strcpy(terminator[1],"CG"); strcpy(terminator[2],"GC");
strcpy(terminator[3],"GG"); strcpy(terminator[4],""); }
else if(num_terminators == 3) { strcpy(terminator[0],"CCC");
strcpy(terminator[1],"CCG"); strcpy(terminator[2],"CGC");
strcpy(terminator[3],"CGG"); strcpy(terminator[4],"GCC");
strcpy(terminator[5],"GCG"); strcpy(terminator[6],"GGC");
strcpy(terminator[7],"GGG"); strcpy(terminator[8],""); }
else { strcpy(terminator[0],""); }
/* num_terminators = num;*/
1403
******
File DISK11:[PRIMER]TEXT.C_ORIGINAL;1
1375
line[0] = '\0'; gets(line); i = 0; num = 0;
n = sscanf(line,"%d",&num);
if(n <= 0) num = 0;
else if(num > 3) { printf("***clamping for 3 bases\n"); num = 3; }
if(num == 1) { strcpy(terminator[0],"C"); strcpy(terminator[1],"G");
strcpy(terminator[2],"");
} else if(num == 2) { strcpy(terminator[0],"CC"); strcpy(terminator[1],"CG");
strcpy(terminator[2],"GC"); strcpy(terminator[3],"GG");
strcpy(terminator[4],"");
} else if(num == 3) { strcpy(terminator[0],"CCC"); strcpy(terminator[1],"CCG");
strcpy(terminator[2],"CGC"); strcpy(terminator[3],"CGG");
strcpy(terminator[4],"GCC"); strcpy(terminator[5],"GCG");
strcpy(terminator[6],"GGC"); strcpy(terminator[7],"GGG");
strcpy(terminator[8],"");
} else { strcpy(terminator[0],""); }
num_terminators = num;
1392
************
************
+----------------------------------------------------------------------------+
| Max-Planck-Institut fuer Phone : +49-761-5108-465 Fax: -221 |
| Immunbiologie PSI : PSI%(0262)45050160374::GARTMANN |
| Postfach 1169 Internet: gartmann at immunbio.mpg.de |
| D-79011 Freiburg, FRG |
+------------- Do you know MENUE, the user environment for VMS? -------------+
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