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ClustalO compile
[jabaws.git]
/
binaries
/
src
/
iupred
/
iupred.c
diff --git
a/binaries/src/iupred/iupred.c
b/binaries/src/iupred/iupred.c
index
2d8b274
..
c5e25a2
100644
(file)
--- a/
binaries/src/iupred/iupred.c
+++ b/
binaries/src/iupred/iupred.c
@@
-85,9
+85,10
@@
int main(int argc, char **argv)
if (argc<2) {
printf(" Usage: %s seqfile type \n",argv[0]);
printf(" where type stands for one of the options of \n");
if (argc<2) {
printf(" Usage: %s seqfile type \n",argv[0]);
printf(" where type stands for one of the options of \n");
- printf(" \"long\", \"short\", \"glob\" or \"all\"\n");
+ printf(" \"long\", \"short\", \"glob\". If no type is provided the program assumes all types\n");
exit(1);
}
exit(1);
}
+
if ((path=getenv("IUPred_PATH"))==NULL) {
fprintf(stderr,"IUPred_PATH environment variable is not set\n");
path="./";
if ((path=getenv("IUPred_PATH"))==NULL) {
fprintf(stderr,"IUPred_PATH environment variable is not set\n");
path="./";
@@
-105,8
+106,10
@@
int main(int argc, char **argv)
printf("#\n");
printf("#\n");
printf("#\n");
printf("#\n");
-
- if ((strncmp(argv[2],"long",4))==0) {
+ if(argv[2]==NULL) {
+ type=3;
+ }
+ else if ((strncmp(argv[2],"long",4))==0) {
type=0;
}
else if ((strncmp(argv[2],"short",5))==0) {
type=0;
}
else if ((strncmp(argv[2],"short",5))==0) {
@@
-115,22
+118,23
@@
int main(int argc, char **argv)
else if ((strncmp(argv[2],"glob",4))==0) {
type=2;
}
else if ((strncmp(argv[2],"glob",4))==0) {
type=2;
}
- else if ((strncmp(argv[2],"all",3))==0) {
- type=3;
- }
else {
else {
- printf("No disorder type is given assuming long\n");
+ printf("Cannot recognise disorder type assuming long\n");
type=0;
}
type=0;
}
+ FILE *fasta;
+
+ if ((fasta=fopen(argv[1],"r"))==NULL) {
+ printf("Could not open %s\n",argv[1]),exit(1);
+ }
+
/* Creating output files depending on the type */
createOutputFiles(type);
/* Creating output files depending on the type */
createOutputFiles(type);
-
/* Read input file sequence by sequence */
/* Read input file sequence by sequence */
- FILE *fasta;
+
SEQS *fastaseq;
SEQS *fastaseq;
- fasta = fopen(argv[1], "r");
do {
do {