+++ /dev/null
-/*
- * cmdargs.c
- *
- * $Id$
- *
- *****************************************************************************
- *
- * Copyright (c) 2004, Luke Sheneman
- * All rights reserved.
- *
- * Redistribution and use in source and binary forms, with or without
- * modification, are permitted provided that the following conditions
- * are met:
- *
- * + Redistributions of source code must retain the above copyright
- * notice, this list of conditions and the following disclaimer.
- * + Redistributions in binary form must reproduce the above copyright
- * notice, this list of conditions and the following disclaimer in
- * the documentation and/or other materials provided with the
- * distribution.
- * + The names of its contributors may not be used to endorse or promote
- * products derived from this software without specific prior
- * written permission.
- *
- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
- * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
- * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
- * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
- * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
- * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
- * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
- * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
- * POSSIBILITY OF SUCH DAMAGE.
- *
- *****************************************************************************
- *
- * AUTHOR:
- *
- * Luke Sheneman
- * sheneman@cs.uidaho.edu
- *
- */
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
-#include <time.h>
-
-
-#ifdef USE_GNU
-#include <getopt.h>
-#else
-#include "getopt_long.h"
-#endif /* USE_GNU*/
-
-
-#include "clearcut.h"
-#include "cmdargs.h"
-
-
-/*
- * NJ_handle_args() -
- *
- */
-NJ_ARGS *
-NJ_handle_args(int argc,
- char *argv[]) {
-
- static NJ_ARGS nj_args;
- int option_index, c;
-
- optind = 0; //neccasary to read in arguments if code is run more than once
-
- struct option NJ_long_options[] = {
-
- /* These options don't set a flag */
- {"in", required_argument, NULL, 'i'},
- {"out", required_argument, NULL, 'o'},
- {"seed", required_argument, NULL, 's'},
- {"matrixout", required_argument, NULL, 'm'},
- {"ntrees", required_argument, NULL, 'n'},
-
- /* These options set a flag */
- {"verbose", no_argument, &(nj_args.verbose_flag), 1},
- {"quiet", no_argument, &(nj_args.quiet_flag), 1},
- {"distance", no_argument, &(nj_args.input_mode), NJ_INPUT_MODE_DISTANCE},
- {"alignment", no_argument, &(nj_args.input_mode), NJ_INPUT_MODE_ALIGNED_SEQUENCES},
- {"help", no_argument, &(nj_args.help), 1},
- {"version", no_argument, &(nj_args.version), 1},
- {"norandom", no_argument, &(nj_args.norandom), 1},
- {"shuffle", no_argument, &(nj_args.shuffle), 1},
- {"stdin", no_argument, &(nj_args.stdin_flag), 1},
- {"stdout", no_argument, &(nj_args.stdout_flag), 1},
- {"dna", no_argument, &(nj_args.dna_flag), 1},
- {"DNA", no_argument, &(nj_args.dna_flag), 1},
- {"protein", no_argument, &(nj_args.protein_flag), 1},
- {"neighbor", no_argument, &(nj_args.neighbor), 1},
- {"expblen", no_argument, &(nj_args.expblen), 1},
- {"expdist", no_argument, &(nj_args.expdist), 1},
-
- {"jukes", no_argument, &(nj_args.jukes_flag), 1},
- {"kimura", no_argument, &(nj_args.kimura_flag), 1},
-
- {0, 0, 0, 0}
-
- };
-
- /* initializes options to their default */
- nj_args.infilename = NULL;
- nj_args.outfilename = NULL;
- nj_args.matrixout = NULL;
- nj_args.seed = time(0);
- nj_args.verbose_flag = 0;
- nj_args.quiet_flag = 0;
- nj_args.input_mode = NJ_INPUT_MODE_DISTANCE;
- nj_args.help = 0;
- nj_args.version = 0;
- nj_args.norandom = 0;
- nj_args.shuffle = 0;
- nj_args.stdin_flag = 0;
- nj_args.stdout_flag = 0;
- nj_args.dna_flag = 0;
- nj_args.protein_flag = 0;
- nj_args.correction_model = NJ_MODEL_NONE;
- nj_args.jukes_flag = 0;
- nj_args.kimura_flag = 0;
- nj_args.neighbor = 0;
- nj_args.ntrees = 1;
- nj_args.expblen = 0;
- nj_args.expdist = 0;
-
- while(1) {
-
- c = getopt_long(argc,
- argv,
- "i:o:s:m:n:vqduahVSIOrDPjkNeE",
- NJ_long_options,
- &option_index);
- if(c == -1) {
- break;
- }
-//printf("%d\t%d\n", option_index, argc);
-//for (int red = 0; red < argc; red++) { printf("%s\n", argv[red]); }
- switch(c) {
-
- case 0:
- if(NJ_long_options[option_index].flag) {
- break;
- }
-
- printf("option %s", NJ_long_options[option_index].name);
- if(optarg) {
- printf(" with arg %s", optarg);
- }
- printf("\n");
- break;
-
- case 'i':
- nj_args.infilename = optarg;
- break;
-
- case 'o':
- nj_args.outfilename = optarg;
- break;
-
- case 's':
- nj_args.seed = atoi(optarg);
- break;
-
- case 'm':
- nj_args.matrixout = optarg;
- break;
-
- case 'n':
- nj_args.ntrees = atoi(optarg);
- break;
-
- case 'v':
- nj_args.verbose_flag = 1;
- break;
-
- case 'q':
- nj_args.quiet_flag = 1;
- break;
-
- case 'd':
- nj_args.input_mode = NJ_INPUT_MODE_DISTANCE;
- break;
-
- case 'a':
- nj_args.input_mode = NJ_INPUT_MODE_ALIGNED_SEQUENCES;
- break;
-
- case 'h':
- nj_args.help = 1;
- break;
-
- case 'V':
- nj_args.version = 1;
- break;
-
- case 'S':
- nj_args.shuffle = 1;
- break;
-
- case 'I':
- nj_args.stdin_flag = 1;
- break;
-
- case 'O':
- nj_args.stdin_flag = 1;
- break;
-
- case 'r':
- nj_args.norandom = 1;
- break;
-
- case 'D':
- nj_args.dna_flag = 1;
- break;
-
- case 'P':
- nj_args.protein_flag = 1;
- break;
-
- case 'j':
- nj_args.jukes_flag = 1;
- break;
-
- case 'k':
- nj_args.kimura_flag = 1;
- break;
-
- case 'N':
- nj_args.neighbor = 1;
- break;
-
- case 'e':
- nj_args.expblen = 1;
- break;
-
- case 'E':
- nj_args.expdist = 1;
- break;
-
- default:
- NJ_usage();
- exit(-1);
- }
- }
-
- if(optind < argc) {
- fprintf(stderr, "Clearcut: Unknown command-line argument:\n --> %s\n", argv[optind]);
- NJ_usage();
- exit(-1);
- }
-
- if(nj_args.version) {
- printf("Clearcut Version: %s\n", NJ_VERSION);
- //exit(0);
- }
-
- if(nj_args.help) {
- NJ_usage();
- //exit(0);
- }
-
- /* if stdin & explicit filename are specified for input */
- if(nj_args.stdin_flag) {
- if(nj_args.infilename) {
- fprintf(stderr, "Clearcut: Ambiguous input source specified. Specify input filename OR stdin.\n");
- NJ_usage();
- exit(-1);
- }
- }
-
- /* if stdout & explicit filename are specified for output */
- if(nj_args.stdout_flag) {
- if(nj_args.outfilename) {
- fprintf(stderr, "Clearcut: Ambiguous output specified. Specify output filename OR stdout.\n");
- NJ_usage();
- exit(-1);
- }
- }
-
- /* if user did not specify stdin or filename, default to stdin */
- if(!nj_args.stdin_flag) {
- if(!nj_args.infilename) {
-
- fprintf(stderr, "Clearcut: No input file specified. Using stdin.\n");
- nj_args.stdin_flag = 1;
- }
- }
-
- /* if user did not specify stdout or filename, default to stdout */
- if(!nj_args.stdout_flag) {
- if(!nj_args.outfilename) {
-
- fprintf(stderr, "Clearcut: No output file specified. Using stdout.\n");
- nj_args.stdout_flag = 1;
- }
- }
-
- /* User must specify distance matrix or alignment */
- if(nj_args.input_mode == NJ_INPUT_MODE_UNKNOWN) {
- fprintf(stderr, "Clearcut: Must specify input type (--distance | --alignment)\n");
- NJ_usage();
- exit(-1);
- }
-
- /* do not allow protein or DNA options for distance matrix input */
- if(nj_args.input_mode == NJ_INPUT_MODE_DISTANCE) {
- if(nj_args.dna_flag || nj_args.protein_flag) {
- fprintf(stderr, "Clearcut: Ambiguous arguments. (--protein | --DNA) do not apply to distance \n");
- NJ_usage();
- exit(-1);
- }
- }
-
- /* make sure different filenames were specified for input and output */
- if(!nj_args.stdin_flag && !nj_args.stdout_flag) {
-
- if(!strcmp(nj_args.infilename, nj_args.outfilename)) {
- fprintf(stderr, "Clearcut: Input filename and output filename must be unique.\n");
- NJ_usage();
- exit(-1);
- }
- }
-
- /* make sure that user specifies DNA or Protein if dealing with alignment input */
- if(nj_args.input_mode == NJ_INPUT_MODE_ALIGNED_SEQUENCES) {
- if(!nj_args.dna_flag && !nj_args.protein_flag) {
- fprintf(stderr, "Clearcut: Must specify protein or DNA for alignment input.\n");
- NJ_usage();
- exit(-1);
- }
- }
-
- /* make sure that user does not specify both protein and DNA when dealing with alignment input */
- if(nj_args.input_mode == NJ_INPUT_MODE_ALIGNED_SEQUENCES) {
- if(nj_args.dna_flag && nj_args.protein_flag) {
- fprintf(stderr, "Clearcut: Specifying protein and DNA sequences are mutually exclusive options\n");
- NJ_usage();
- exit(-1);
- }
- }
-
- /* make sure verbose and quiet were not specified together */
- if(nj_args.verbose_flag && nj_args.quiet_flag) {
- fprintf(stderr, "Clearcut: Verbose and Quiet mode are mutually exclusive.\n");
- NJ_usage();
- exit(-1);
- }
-
- /* make sure that a correction model was specified only when providing an alignment */
- if(nj_args.input_mode == NJ_INPUT_MODE_DISTANCE) {
- if(nj_args.jukes_flag || nj_args.kimura_flag) {
- fprintf(stderr, "Clearcut: Only specify correction model for alignment input.\n");
- NJ_usage();
- exit(-1);
- }
- } else {
- if(nj_args.jukes_flag && nj_args.kimura_flag) {
- fprintf(stderr, "Clearcut: Only specify one correction model\n");
- NJ_usage();
- exit(-1);
- } else {
- if(nj_args.jukes_flag && !nj_args.kimura_flag) {
- nj_args.correction_model = NJ_MODEL_JUKES;
- } else if(nj_args.kimura_flag && !nj_args.jukes_flag) {
- nj_args.correction_model = NJ_MODEL_KIMURA;
- } else {
- nj_args.correction_model = NJ_MODEL_NONE; /* DEFAULT */
- }
- }
- }
-
- /* make sure that the number of output trees is reasonable */
- if(nj_args.ntrees <= 0) {
- fprintf(stderr, "Clearcut: Number of output trees must be a positive integer.\n");
- NJ_usage();
- exit(-1);
- }
-
- /*
- * make sure that if exponential distances are specified,
- * we are dealing with alignment input
- */
- if(nj_args.expdist && nj_args.input_mode != NJ_INPUT_MODE_ALIGNED_SEQUENCES) {
- fprintf(stderr, "Clearcut: Exponential notation for distance matrix output requires that input be an alignment\n");
- NJ_usage();
- exit(-1);
- }
-
- return(&nj_args);
-}
-
-
-
-
-
-/*
- * NJ_print_args() -
- *
- */
-void
-NJ_print_args(NJ_ARGS *nj_args) {
-
- char input_mode[32];
-
- switch (nj_args->input_mode) {
- case NJ_INPUT_MODE_DISTANCE:
- sprintf(input_mode, "Distance Matrix");
- break;
- case NJ_INPUT_MODE_UNALIGNED_SEQUENCES:
- sprintf(input_mode, "Unaligned Sequences");
- break;
- case NJ_INPUT_MODE_ALIGNED_SEQUENCES:
- sprintf(input_mode, "Aligned Sequences");
- break;
- default:
- sprintf(input_mode, "UNKNOWN");
- break;
- }
-
- printf("\n*** Command Line Arguments ***\n");
-
- printf("Input Mode: %s\n", input_mode);
-
- if(nj_args->stdin_flag) {
- printf("Input from STDIN\n");
- } else {
- printf("Input File: %s\n", nj_args->infilename);
- }
-
- if(nj_args->stdout_flag) {
- printf("Output from STDOUT\n");
- } else {
- printf("Output File: %s\n", nj_args->outfilename);
- }
-
- if(nj_args->input_mode != NJ_INPUT_MODE_DISTANCE) {
- if(nj_args->aligned_flag) {
- printf("Input Sequences Aligned: YES\n");
- } else {
- printf("Input Sequences Aligned: NO\n");
- }
- }
-
- if(nj_args->verbose_flag) {
- printf("Verbose Mode: ON\n");
- } else {
- printf("Verbose Mode: OFF\n");
- }
-
- if(nj_args->quiet_flag) {
- printf("Quiet Mode: ON\n");
- } else {
- printf("Quiet Mode: OFF\n");
- }
-
- if(nj_args->seed) {
- printf("Random Seed: %d\n", nj_args->seed);
- }
-
- printf("\n*******\n");
-
- return;
-}
-
-
-
-
-/*
- * NJ_usage() -
- *
- * Print a usage message
- *
- */
-void
-NJ_usage(void) {
-
- printf("Usage: clearcut --in=<infilename> --out=<outfilename> [options]...\n");
- printf("GENERAL OPTIONS:\n");
- printf(" -h, --help Display this information.\n");
- printf(" -V, --version Print the version of this program.\n");
- printf(" -v, --verbose More output. (Default: OFF)\n");
- printf(" -q, --quiet Silent operation. (Default: ON)\n");
- printf(" -s, --seed=<seed> Explicitly set the PRNG seed to a specific value.\n");
- printf(" -r, --norandom Attempt joins deterministically. (Default: OFF)\n");
- printf(" -S, --shuffle Randomly shuffle the distance matrix. (Default: OFF)\n");
- printf(" -N, --neighbor Use traditional Neighbor-Joining algorithm. (Default: OFF)\n");
-
- printf("\n");
- printf("INPUT OPTIONS:\n");
- printf(" -I, --stdin Read input from STDIN.\n");
- printf(" -d, --distance Input file is a distance matrix. (Default: ON)\n");
- printf(" -a, --alignment Input file is a set of aligned sequences. (Default: OFF)\n");
- printf(" -D, --DNA Input alignment are DNA sequences.\n");
- printf(" -P, --protein Input alignment are protein sequences.\n");
-
- printf("\n");
- printf("CORRECTION MODEL FOR COMPUTING DISTANCE MATRIX (Default: NO Correction):\n");
- printf(" -j, --jukes Use Jukes-Cantor correction for computing distance matrix.\n");
- printf(" -k, --kimura Use Kimura correction for distance matrix.\n");
-
- printf("\n");
- printf("OUTPUT OPTIONS:\n");
- printf(" -O, --stdout Output tree to STDOUT.\n");
- printf(" -m, --matrixout=<file> Output distance matrix to specified file.\n");
- printf(" -n, --ntrees=<n> Output n trees. (Default: 1)\n");
- printf(" -e, --expblen Exponential notation for branch lengths. (Default: OFF)\n");
- printf(" -E, --expdist Exponential notation in distance output. (Default: OFF)\n");
-
- printf("\n");
- printf("EXAMPLES:\n");
- printf(" Compute tree by supplying distance matrix via stdin:\n");
- printf(" clearcut --distance < distances.txt > treefile.tre\n");
- printf("\n");
- printf(" Compute tree by supplying an alignment of DNA sequences from a file:\n");
- printf(" clearcut --alignment --DNA --in=alignment.txt --out=treefile.tre\n");
-
- return;
-}
-
-
-
projects / mothur.git / blobdiff