/***************************************************************************** ****************************************************************************** ****************************************************************************** ***** ***** ***** PROGRAM 01_TO_RS v1.0 ***** ***** A program for converting 0/1 matrix data to RESTSITE format. ***** ***** Copyright (c) 1991 by Joyce C. Miller. All Rights Reserved. ***** ***** ***** ***** This program converts data from a 0/1 matrix (used by PAUP, ***** ***** McClade, and Principal Component Analysis programs) into a format ***** ***** usable by RESTSITE. From the command line, it reads in the name ***** ***** of an ASCII text file containing the square 0/1 data matrix, the ***** ***** name of the output file (for the RESTSITE data), the name of an ***** ***** ASCII text file with the names of the OTUs and characters found in ***** ***** the 0/1 matrix, and the matrix type. For more information on the ***** ***** formats of these files, see the program documentation. ***** ***** ***** ***** PAUP by David Swofford, Copyright (c) 1989 by Illinois Natural ***** ***** History Survey. All Rights Reserved. ***** ***** McCLADE Copyright (c) 1989 by Wayne Maddison and David Maddison. ***** ***** All Rights Reserved. ***** ***** ***** ***** List of C functions used in this program: ***** ***** ***** ***** FUNCTION LIBRARY FUNCTION LIBRARY ***** ***** fclose stdio.h feof stdio.h ***** ***** fgetc stdio.h fgets stdio.h ***** ***** fopen stdio.h fprintf stdio.h ***** ***** fread stdio.h fseek stdio.h ***** ***** fwrite stdio.h printf stdio.h ***** ***** rewind stdio.h sscanf stdio.h ***** ***** strcpy string.h strcmp string.h ***** ***** system stdlib.h ***** ***** ***** ****************************************************************************** ****************************************************************************** *****************************************************************************/ /***************************************************************************** ** INCLUDE FILES ** *****************************************************************************/ #include #include #include #include /* file containing type definitions & constants */ #include /* file containing error messages */ #include /* file containing some commonly-used functions */ /***************************************************************************** ** TYPE DEFINITIONS & SYMBOLIC CONSTANTS ** *****************************************************************************/ #define VNUM 1.0 /* version number of this program */ #define YEAR 1991 /* calendar year this version was released */ #define goodx ((x=='0')||(x=='1')||(x=='-')||(x=='X')||(x=='x')||(x=='?')) #define diffprb (strcmp(p1.prb,p2.prb) != 0) /* are probes names different? */ #define diffenz (strcmp(p1.enz,p2.enz) != 0) /* are enzymes different? */ #define diffrv (p1.rv != p2.rv) /* are r-values different? */ #define diffprobe (diffprb || diffenz || diffrv) /* are PECs different? */ typedef struct { /* structure to hold informaton on one individual */ otuname idnum; /* identification number */ otuname K1; /* key #1 */ otuname K2; /* key #2 */ otuname K3; /* key #3 */ otuname K4; /* key #3 */ } indinfo; typedef struct { /* holds information on one probr/enzyme combination */ char prb[PRBLEN]; /* probe name */ char enz[ENZLEN]; /* enzyme name */ float rv; /* size of restriction site */ float fs; /* fragment/site */ } prbinfo; /***************************************************************************** ** FUNCTION PROTOTYPES ** *****************************************************************************/ void makelists(char ipfl[]); /* converts ind&prb info to 2 binary files */ void flipmat(char mtfl[], char mattype); /* flips matrix type 2 to 1 */ void convert(char rsfl[]); /* converts type 1 matrix to RESTSITE format */ /***************************************************************************** ** GLOBAL VARIABLES ** *****************************************************************************/ int ni = 0; /* number of OTUs */ int nc = 0; /* number of characters */ /***************************************************************************** ****************************************************************************** ****************************************************************************** ****** ****** ****** MAIN PROGRAM ****** ****** ****** ****************************************************************************** ****************************************************************************** ****************************************************************************** ***** This section of the program prints out the program name and a ***** ***** copyright message, then error-checks the command line. Then the ***** ***** rest of the program is executed. ***** ***** ***** ***** Functions called: ***** ***** makelists -- takes the ASCII file with the names of the OTUs ***** ***** and the probes, and converts the information to ***** ***** two binary files. ***** ***** flipmat -- flips 0/1 matrix from type 2 to type 1 if needed.***** ***** convert -- converts type 1 matrix to RESTSITE format. ***** *****************************************************************************/ void main(int argc,char *argv[]) { printf("\r\nProgram 01_TO_RS v%3.1f\r\n",VNUM); /* message to user */ printf("A program for converting data in 0/1 matrices to RESTSITE format."); printf("\r\nCopyright (c) %d by Joyce C. Miller. ",YEAR); printf("All Rights Reserved.\r\n"); if (argc < 5) { /* error if command line incomplete */ printf("\a\r\nError 101: The proper format of the command line should "); printf("be:\r\n\n 01_TO_RS 01FILE RSFILE OTUFILE "); printf("MATRIXTYPE\r\n\n All of these items are necessary. "); printf(" Refer to the\r\n documentation if you require "); printf("more information.\r\n"); exit(0); } makelists(argv[3]); /* converts OTU & probe info to binary */ flipmat(argv[1],argv[4][0]); /* flips type 2 matrix to type 1 */ convert(argv[2]); /* converts 0/1 data to RESTSITE format */ system("DEL !@!.0"); /* delete temporary files */ system("DEL !@!.1"); system("DEL !@!.2"); } /* END OF FUNCTION MAIN */ /***************************************************************************** ** ** ** FUNCTION MAKELISTS ** ** ** ** This function is called from FUNCTION MAIN, and reads in the list of OTU ** ** and probe names. First, the file is opened, and the first line is read, ** ** and the number of individuals and the number of characters are read in. ** ** Then, information on that many individuals is read, and written to a ** ** temporary file. The character information is sent to a separate file. ** ** Control then passes back to FUNCTION MAIN. ** ** ** ** Functions called: ** ** opntrdfl -- opens a text file for reading. ** ** opnbwtfl -- opens a binary file for writing. ** ** rserror311 -- error message if error reading datafile. ** ** rserror323 -- error message if error writing to temp file. ** *****************************************************************************/ void makelists(char ipfl[]) { char tempstr[MAXSTRLEN]; /* temporary string */ char tn[MAXSTRLEN]; /* temporary string */ FILE *fpi, *fpd; /* file pointers */ register int i; /* loop control variable */ indinfo in; /* structure to hold information on one individual */ prbinfo pi; /* structure to hold information on one probe */ printf("\r\nRecovering list of OTUs and characters"); fpi = opntrdfl(fpi,ipfl); /* open ASCII file for reading */ if ((fgets(tempstr,MAXSTRLEN,fpi)) == NULL) rserror311(ipfl); sscanf(tempstr,"%d %d",&ni,&nc); /* get # individuals & probes */ fpd = opnbwtfl(fpd,"!@!.1"); /* open binary file for individual data */ for(i=0; i