static char const rcsid [] = "$Id: plor.c,v 1.1 1998/04/21 10:50:03 stojanov Exp $"; /*****************************************************************************/ /* */ /* Program: plor (data reorganization of plain format landmarks files) */ /* */ /* Author: Nikola Stojanovic */ /* */ /* Revision: 16 APR 97 Version 1.0 */ /* */ /* */ /* Given a file in "plain" format, the program reorganizes and outputs */ /* lines of data, either as default or with respect to the provided pattern */ /* of output */ /* */ /*****************************************************************************/ #include #include #include #include "ntl.h" /*****************************************************************************/ /* */ /* Definitions section */ /* */ /*****************************************************************************/ /*****************************************************************************/ /* Definitions of the constants of the program unit */ /*****************************************************************************/ #define DEFAULT_TEMPLATE "set" /*****************************************************************************/ /* Prototypes of locally used functions of the program unit */ /*****************************************************************************/ void plor_output_data (plain_ptr records, char *template); /*****************************************************************************/ /* */ /* Code section */ /* */ /*****************************************************************************/ /*****************************************************************************/ /* */ /* Procedure: main */ /* */ /* "main" procedure of the program. Receives and analyses the command line */ /* parameters, sets the control variables of the program, checksir */ /* consistency and passes control to internal procedures which actually */ /* process the input data and output results; returns 0 if everything is */ /* OK, non-zero status in case of any errors */ int main (int argc, char **argv) { char *input_file, *template; bool template_set; int arg_count, scan; plain_ptr records; errind report; input_file = NULL; template_set = FALSE; template = DEFAULT_TEMPLATE; if (argc < 2) { /* Display instructions and terminate */ fprintf (stderr, "usage: %s \n", argv [0]); fprintf (stderr, " [-o ]\n"); exit (1); } else { /* Some parameters provided - process them */ /* Proceed to extract the command line parameters and create the settings */ arg_count = 1; while (arg_count < argc) { if (argv [arg_count] [0] != '-') { /* Not an "-" option - file name */ if (input_file != NULL) { fprintf (stderr, "Input file already set.\n"); exit (1); } else { input_file = NTL0_strsave (argv [arg_count]); arg_count++; } } else if (!strcmp (argv [arg_count], "-o")) { /* Template specification */ arg_count++; if (template_set) { fprintf (stderr, "Output template already set.\n"); exit (1); } else if (arg_count == argc) { fprintf (stderr, "Missing template specification.\n"); exit (1); } else { template = NTL0_strsave (argv [arg_count]); template_set = TRUE; arg_count++; } } else { /* Unknown command-line option */ fprintf (stderr, "Illegal option (%s).\n", argv [arg_count]); fprintf (stderr, "usage: %s \n", argv [0]); fprintf (stderr, " [-o ]\n"); exit (1); } } /* Now check whether all necessary parameters have been provided */ if (input_file == NULL) { fprintf (stderr, "Must have a file to process.\n"); exit (1); } /* Check the legality of the provided template */ if (template == NULL) { fprintf (stderr, "Must have a template to work with - internal error.\n"); exit (1); } else { scan = 0; while (template [scan] != '\0') { if ((template [scan] != 's') && /* Range start output request */ (template [scan] != 'e') && /* Range end output request */ (template [scan] != 'l') && /* Range length output request */ (template [scan] != 't') && /* Sequence text output request */ (template [scan] != 'n') && /* Site name output request */ (template [scan] != 'b') && /* Binding factor output request */ (template [scan] != 'd') && /* Originating database output request */ (template [scan] != 'f') && /* Originating file output request */ (template [scan] != 'm') && /* Matching data output request */ (template [scan] != 'a') && /* Strand output request */ (template [scan] != 'r') && /* Reference output request */ (template [scan] != 'c')) { /* Count output request */ fprintf (stderr, "Illegal specifier ('%c') in the output template.\n", template [scan]); exit (1); } scan++; } } /* Now proceed to load the data from the specified plain format file */ if ((report = NTL2_Load_Plain (input_file, &records)) != NULL) { fprintf (stderr, "Can't open sequences file '%s' (%s).\n", input_file, report -> message); exit (1); } else { /* File loading OK, output the contents */ plor_output_data (records, template); exit (0); } } } /*****************************************************************************/ /* */ /* Procedure: plor_output_data */ /* */ void plor_output_data (plain_ptr records, char *template) { plain_ptr data_scan; int template_scan; for (data_scan = records; data_scan != NULL; data_scan = data_scan -> next) { template_scan = 0; while (template [template_scan] != '\0') { if (template [template_scan] == 's') { /* Range start output */ printf ("%ld", data_scan -> start); } else if (template [template_scan] == 'e') { /* Range end output */ printf ("%ld", data_scan -> stop); } else if (template [template_scan] == 'l') { /* Range length output */ if (data_scan -> text == NULL) printf ("%ld", (data_scan -> stop) - (data_scan -> start) + 1); else printf ("%d", (int) (strlen (data_scan -> text))); } else if (template [template_scan] == 't') { /* Sequence text output */ if (data_scan -> text == NULL) printf ("null"); else printf ("%s", data_scan -> text); } else if (template [template_scan] == 'n') { /* Site name output */ if (data_scan -> site == NULL) printf ("null"); else printf ("%s", data_scan -> site); } else if (template [template_scan] == 'b') { /* Binding factor output */ if (data_scan -> binding == NULL) printf ("null"); else printf ("%s", data_scan -> binding); } else if (template [template_scan] == 'd') { /* Database output */ if (data_scan -> database == NULL) printf ("null"); else printf ("%s", data_scan -> database); } else if (template [template_scan] == 'f') { /* Originating file output */ if (data_scan -> file == NULL) printf ("null"); else printf ("%s", data_scan -> file); } else if (template [template_scan] == 'm') { /* Matching data output */ if (data_scan -> matched == NULL) printf ("null"); else printf ("%s", data_scan -> matched); } else if (template [template_scan] == 'a') { /* Strand output */ printf ("%c", data_scan -> strand); } else if (template [template_scan] == 'r') { /* Reference output */ if (data_scan -> reference == NULL) printf ("null"); else printf ("%s", data_scan -> reference); } else if (template [template_scan] == 'c') { /* Count output */ if (data_scan -> c_range == NULL) printf ("null"); else printf ("%s", data_scan -> c_range); } template_scan++; if (template [template_scan] != '\0') printf (" "); else printf ("\n"); } } }