416 lines
8.6 KiB
C
416 lines
8.6 KiB
C
#include <stdio.h>
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#define USER_DATA
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#ifdef USER_DATA
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#include <pwd.h>
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#endif
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#include "misc.h" /* IMPORT: is_file */
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/*
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** This is an incredible hack. The original is based on a csh script
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** Beware of horrid goto's etc
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*/
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typedef char String[200];
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String SUBCLONES; /* initialised in initialise() */
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String methods[] = {
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"shear",
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"Sau3A",
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"Alu-1",
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};
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String vectors[] = {
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"M13",
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"pBS",
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"pEMBL9",
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"pUC118",
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};
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String sizes[] = {
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"1-2",
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"6-9",
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"6-9",
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"9-14",
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};
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int MATCH = 3;
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/*
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** Defaults
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*/
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String def_mtd;
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String def_cosmid;
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String def_method;
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String def_vector;
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String def_size;
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String def_verify;
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/*
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** Answers
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*/
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String ans_mtd;
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String ans_cosmid;
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String ans_method;
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String ans_vector;
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String ans_size;
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#define MAX_COMMENTS 10
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String ans_comments[MAX_COMMENTS];
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int comments;
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String ans_verify;
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static void initialise()
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/*
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** Initialise miscellaneous variables
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*/
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{
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char *subclones;
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/* clonelib = subclones:$SUBCLONES */
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if (is_file("subclones"))
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strcpy(SUBCLONES,"subclones");
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else {
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subclones = (char *) getenv("SUBCLONES");
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if (subclones == NULL)
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SUBCLONES[0] = '\0';
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else if (is_file(subclones))
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strcpy(SUBCLONES,subclones);
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else
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SUBCLONES[0] = '\0';
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}
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}
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int set_defaults()
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{
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FILE *f;
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String line;
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String last_cosmid;
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String max_mtd;
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String mtd;
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String alpha;
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int number;
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int i;
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/* Determine SUBCLONES */
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initialise();
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if ( (f = fopen(SUBCLONES,"r")) == NULL ) return 1;
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max_mtd[0] = '\0';
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while ( fgets(line,sizeof(line),f) ) {
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sscanf(line, "%s %s", mtd,last_cosmid);
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if (strcmp(max_mtd,mtd) < 0) strcpy(max_mtd,mtd);
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}
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if ( ! max_mtd[0] ) return 1;
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/*
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** generate next number
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*/
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for (i = 0;isalpha(max_mtd[i]);i++) alpha[i] = max_mtd[i];
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alpha[i] = '\0';
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number = atoi(&max_mtd[i]) + 1;
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sprintf(def_mtd,"%s%02d",alpha,number);
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strcpy(def_cosmid, last_cosmid);
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strcpy(def_method, methods[0]);
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strcpy(def_vector, vectors[0]);
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strcpy(def_size, sizes[0]);
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strcpy(def_verify, "Yes");
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return 0;
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}
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ask_mtd()
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{
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ask:
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printf("Microtitre dish [%s] ? ",def_mtd);
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gets(ans_mtd);
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if (strcmp(ans_mtd,"?")==0) {
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printf("* Enter the name of the new microtitre dish to be added to the library.\n");
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printf(" A microtitre dish must be a letter followed by two digits. Eg a87\n");
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goto ask;
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} else if (ans_mtd[0]) {
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if (! islower(ans_mtd[0]) ||
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(strlen(ans_mtd)==3 ?
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! isdigit(ans_mtd[1]) :
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! islower(ans_mtd[1])) ||
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! isdigit(ans_mtd[2]) ||
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(strlen(ans_mtd)==3 ?
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ans_mtd[3] :
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! isdigit(ans_mtd[3]) ||
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ans_mtd[4])) {
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printf("! Invalid microtitre dish name.\n");
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printf(" A microtitre dish must be a letter followed by two digits. Eg a87\n");
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goto ask;
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}
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} else {
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strcpy(ans_mtd,def_mtd);
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}
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}
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ask_cosmid()
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{
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ask:
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printf ("Cosmid [%s] ? ",def_cosmid);
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gets(ans_cosmid);
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if ( strcmp(ans_cosmid,"?") == 0 ) {
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printf("* Enter the name of the cosmid from which the subclones was made.\n");
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printf(" NO check is made on the correctness of the value entered.\n");
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goto ask;
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} else if ( ans_cosmid[0] ){
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int i;
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for (i=0; i<strlen(ans_cosmid); i++) {
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if (i) {
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if (! isupper(ans_cosmid[i]) &&
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! isdigit(ans_cosmid[i])) break;
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} else {
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if (! isupper(ans_cosmid[i])) break;
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}
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}
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if (i != strlen(ans_cosmid)) {
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printf("! Invalid cosmid name.\n");
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printf(" A cosmid must be an letter followed by alphanumeric characters only\n");
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goto ask;
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}
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} else {
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strcpy(ans_cosmid,def_cosmid);
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}
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}
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#define N(A) ( sizeof(A) / sizeof(A[0]) )
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ask_method()
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{
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ask:
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printf("Method of fragmentation [%s] ? ",def_method);
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gets(ans_method);
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if ( strcmp(ans_method,"?") == 0) {
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int i;
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printf("* Enter the fragmentation method used to make the subclones\n");
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printf(" Enter one of:\n");
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printf(" ");
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for (i=0; i< N(methods); i++)
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printf("%s ",methods[i]);
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printf("\n");
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goto ask;
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} else if (ans_method[0]) {
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int i;
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for (i=0; i<N(methods);i++) {
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if ( strncmp(ans_method,methods[i],MATCH) == 0) {
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strcpy(ans_method,methods[i]);
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break;
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}
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}
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if (i == N(methods)) {
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printf("! Invalid fragmentation method\n");
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printf(" A valid fragmentation method is one of:\n");
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printf(" ");
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for (i=0; i< N(methods); i++)
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printf("%s ",methods[i]);
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printf("\n");
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goto ask;
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}
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} else {
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strcpy(ans_method, def_method);
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}
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}
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ask_vector()
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{
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ask:
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printf("Vector [%s] ? ",def_vector);
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gets(ans_vector);
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if ( strcmp(ans_vector,"?") == 0) {
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int i;
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printf("* Enter the vector being used for the subclones\n");
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printf(" Enter one of:\n");
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printf(" ");
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for (i=0; i< N(vectors); i++)
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printf("%s ",vectors[i]);
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printf("\n");
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goto ask;
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} else if (ans_vector[0] ) {
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int i;
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for (i=0; i<N(vectors);i++) {
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if ( strncmp(ans_vector,vectors[i],MATCH) == 0) {
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strcpy(ans_vector,vectors[i]);
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strcpy(def_size,sizes[i]);
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break;
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}
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}
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if (i == N(vectors)) {
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printf("! Invalid fragmentation method\n");
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printf(" A valid fragmentation method is one of:\n");
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printf(" ");
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for (i=0; i< N(vectors); i++)
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printf("%s ",vectors[i]);
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printf("\n");
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goto ask;
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}
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} else {
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strcpy(ans_vector, def_vector);
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}
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}
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ask_size()
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{
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ask:
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printf("Size range [%s] ? ",def_size);
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gets(ans_size);
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if (strcmp(ans_size,"?") == 0) {
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printf("* Enter the size of the insert in the vector\n");
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printf(" The size should be a range in kilobases\n");
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printf(" Eg 1-2\n");
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goto ask;
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} else if (ans_size[0]) {
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int i;
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for (i=0; isdigit(ans_size[i]); i++);
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if (ans_size[i] == '-') {
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for (i++; isdigit(ans_size[i]); i++);
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}
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if (i != strlen(ans_size)) {
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printf("! Invalid size range specification.\n");
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printf(" The size range should be a range in kilobases. Eg 1-2\n");
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goto ask;
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}
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} else {
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strcpy(ans_size, def_size);
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}
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}
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ask_comments()
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{
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int i;
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String ans_comment;
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for (i=0; i<MAX_COMMENTS; i++) ans_comments[i][0] = '\0';
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comments = 0;
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ask:
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printf("Comment #%d [] ? ",comments+1);
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gets(ans_comment);
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if (strcmp(ans_comment,"?") == 0) {
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printf("* Enter a one line comment.\n");
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printf(" Multiple comments can be entered. When you wish to have entered all the\n");
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printf(" comments you wish, press return to the comment prompt.\n");
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goto ask;
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} else if (ans_comment[0]) {
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strcpy(ans_comments[comments++],ans_comment);
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if (comments == MAX_COMMENTS) {
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printf("! Maximum number if comments reached. Sorry.\n");
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} else
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goto ask;
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}
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}
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ask_verify()
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{
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int i;
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printf("\nHere are the values you entered:\n\n");
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printf("Microtitre dish number: %s\n", ans_mtd);
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printf("Cosmid: %s\n", ans_cosmid);
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printf("Fragmentation method: %s\n", ans_method);
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printf("Vector: %s\n", ans_vector);
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printf("Size range: %s\n", ans_size);
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for(i=0; i< comments; i++)
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printf("Comment: #%d %s\n", i+1, ans_comments[i]);
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printf("\n");
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ask:
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printf("Are these values correct [%s] ? ", def_verify);
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gets(ans_verify);
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if (strcmp(ans_verify,"?") == 0 ) {
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printf("Enter `Yes' if these values are correct. They will then be appended to the\n");
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printf("subclone libraries file.\n");
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printf("Enter `No' to exit the program.\n");
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goto ask;
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} else if (ans_verify[0]) {
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if ( strchr("YyNn",ans_verify[0]) == NULL ) {
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printf("Please enter `Yes' or `No'.\n");
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goto ask;
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}
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} else {
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strcpy(ans_verify, def_verify);
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}
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}
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update()
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{
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FILE *f;
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int i;
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String output;
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#ifdef USER_DATA
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struct passwd *pw;
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#endif
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if ( (f = fopen(SUBCLONES,"a")) == NULL) return 1;
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fprintf(f,"%s %s %s %s %s", ans_mtd, ans_cosmid, ans_size, ans_method, ans_vector);
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for (i=0; i< comments; i++)
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fprintf(f," (%s)", ans_comments[i]);
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#ifdef USER_DATA
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pw = getpwuid(getuid());
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fprintf(f," # %s",pw->pw_name);
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shell_call("hostname",output, sizeof(output));
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fprintf(f," %s",output);
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shell_call("date",output, sizeof(output));
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fprintf(f," %s",output);
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#endif
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fprintf(f,"\n");
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fclose(f);
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return 0;
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}
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main ()
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{
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printf("Maintain subclone database\n\n");
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if ( set_defaults() ) {
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fprintf (stderr,"Cannot open file %s\n",SUBCLONES);
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exit(1);
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}
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printf("Database=%s\n\n",SUBCLONES);
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ask_mtd();
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ask_cosmid();
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ask_method();
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ask_vector();
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ask_size();
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ask_comments();
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ask_verify();
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if ( strchr("Yy",ans_verify[0]) != NULL) {
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printf("Updating file %s with new values...",SUBCLONES);
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update();
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printf("done\n");
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} else {
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printf("No update made\n");
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}
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}
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