+++ /dev/null
-
-#include "string.h"
-#include "stdio.h"
-#include "stdlib.h"
-#include "fastal_lib_header.h"
-
-
-void
-tree_parse(struct Fastal_arguments *arguments, char* param)
-{
- char delims[] = "";
- arguments->tree_method = strtok(param,delims);
- if (arguments->tree_method == "parttree")
- {
- arguments->tree_param1 = 6;
- arguments->tree_param2 = 150;
- }
- char *tmp = strtok(NULL,delims);
- if (tmp != NULL)
- {
- arguments->tree_param1 = atoi(tmp);
- arguments->tree_param2 = atoi(strtok(NULL,delims));
- }
-// printf("A: %s %i %i", arguments->tree_method, arguments->tree_param1, arguments->tree_param2);
-}
-
-
-
-void
-arg_parse (int argc, char **argv, struct Fastal_arguments *arguments)
-{
-// default values
-
- arguments->diag_method = "blast";
- arguments->output_file = "out->aln";
- arguments->tree_file = NULL;
- arguments->gep = -1;
- arguments->gop = -10;
- arguments->method = "fast";
- arguments->tree_method = "oligotree";
- arguments->mat="dna_idmat";
- arguments->tree_only = 0;
- arguments->evaluate = 0;
- arguments->score = 0;
-// arguments->retree = 0;
- arguments->agreement_score = 0;
- arguments->num_ref_aln = 0;
- arguments->is_dna = 1;
- arguments->aln_ref = NULL;
- arguments->aln2test = NULL;
- arguments->tree_out = 0;
- arguments->gap_iterate = 0;
-
-
- int i = 1;
- char *param;
-
- for (i = 0; i < argc; ++i)
- {
- param = argv[i];
- if ( ( !strcmp(param, "-d" )) || ( !strcmp(param, "--is_dna")))
- {
- arguments->is_dna = 1;
- arguments->mat = "dna_idmat";
- }
- else if ( ( !strcmp(param, "-a" )) || ( !strcmp(param, "--is_aa")))
- {
- arguments->is_dna = 0;
- arguments->mat = "blosum62mt";
-
- }
-// printf("%s\n", arguments->mat);
- }
- if (arguments->is_dna)
- {
- arguments->tree_param1 = 2;
- arguments->tree_param2 = 5;
- }
- else
- {
- arguments->tree_param1 = 1;
- arguments->tree_param2 = 10;
- }
-
-
- i = 1;
- while (i < argc)
- {
- param = argv[i];
- if ( ( !strcmp(param, "-i" )) || ( !strcmp(param, "--in")))
- {
- arguments->sequence_file = argv[++i];
- }
- else if ( ( !strcmp(param, "-t" )) || ( !strcmp(param, "--tree_file")))
- {
- arguments->tree_file = argv[++i];
- }
- else if ( !strcmp(param, "--mat"))
- {
- arguments->mat = argv[++i];
- }
- else if ( !strcmp(param, "--tree_method"))
- {
- tree_parse(arguments, argv[++i]);
-// arguments->tree_file = argv[++i];
- }
- else if ( ( !strcmp(param, "-o" )) || ( !strcmp(param, "--outfile")))
- {
- arguments->output_file = argv[++i];
- }
- else if ( ( !strcmp(param, "-m" )) || ( !strcmp(param, "--method")))
- {
- ++i;
- if ( (!strcmp(argv[i], "fast")) || (!strcmp(argv[i], "nw")) || (!strcmp(argv[i], "gotoh")) || (!strcmp(argv[i], "udisc")) )
- arguments->method = argv[i];
- else
- {
- printf("Method %s unknown\n", argv[i]);
- exit(1);
- }
- }
- else if ( ( !strcmp(param, "-b" )) || ( !strcmp(param, "--diag_method")))
- {
- ++i;
- if ( (!strcmp(argv[i], "blast")) || (!strcmp(argv[i], "blastz")) || (!strcmp(argv[i], "blat")) || (!strcmp(argv[i], "ktup")))
- arguments->diag_method = argv[i];
- else
- {
- printf("DIAG Method %s unknown\n", argv[i]);
- exit(1);
- }
- }
- else if ( ( !strcmp(param, "-d" )) || ( !strcmp(param, "--is_dna")))
- {
- arguments->is_dna = 1;
- }
- else if ( ( !strcmp(param, "-a" )) || ( !strcmp(param, "--is_aa")))
- {
- arguments->is_dna = 0;
- }
- else if ( ( !strcmp(param, "-g" )) || ( !strcmp(param, "--gop")))
- {
- arguments->gop = atof(argv[++i]);
- }
-// else if ( ( !strcmp(param, "-r" )) || ( !strcmp(param, "--retree")))
-// {
-// arguments->retree = atoi(argv[++i]);
-// }
- else if ( ( !strcmp(param, "-e" )) || ( !strcmp(param, "--gep")))
- {
- arguments->gep = atof(argv[++i]);
- }
- else if ( ( !strcmp(param, "-k" )) || ( !strcmp(param, "--p1")))
- {
- arguments->tree_param1 = atoi(argv[++i]);
- }
- else if ( ( !strcmp(param, "-c" )) || ( !strcmp(param, "--p2")))
- {
- arguments->tree_param2 = atoi(argv[++i]);
- }
- else if ( !strcmp(param, "--eval_aln"))
- {
- arguments->evaluate = 1;
- }
- else if ( ( !strcmp(param, "-s" )) || ( !strcmp(param, "--score")))
- {
- arguments->score = 1;
- }
- else if ( !strcmp(param, "--tree_out"))
- {
- arguments->tree_out = 1;
- }
- else if ( !strcmp(param, "--tree_only"))
- {
- arguments->tree_only = 1;
- }
- else if ( !strcmp(param, "--agreement_score"))
- {
- arguments->agreement_score = 1;
- }
- else if ( !strcmp(param, "--make_ref_aln"))
- {
- arguments->num_ref_aln = atoi(argv[++i]);
- arguments->num_seq_in_ref = atoi(argv[++i]);
- }
- else if ( !strcmp(param, "--aln_ref"))
- {
- arguments->aln_ref = argv[++i];
- }
- else if ( !strcmp(param, "--gap_iterate"))
- {
- arguments->gap_iterate = atoi(argv[++i]);
- }
- else if ( !strcmp(param, "--aln2test"))
- {
- arguments->aln2test = argv[++i];
- }
- else if ( ( !strcmp(param, "-h" )) || ( !strcmp(param, "--help")) || ( !strcmp(param, "-?" )))
- {
- printf("Fastal - a fast alignment tool\n");
- printf("-i --in The sequence_file\n");
- printf("-t --tree_file The treefile\n");
- printf(" --tree_method The method to produce the tree:\n");
- printf(" oligo - very fast method\n");
- printf(" parttree - method like in mafft\n");
- printf("-o --outfile The output file\n");
- printf("-m --method The method to use:\n");
- printf(" fast - fast approximate algorithm [default]\n");
- printf(" nw - needleman-wunsch\n");
- printf(" gotoh - gotoh\n");
- printf("-d --is_dna Sequence are DNA\n");
- printf("-a --is_aa Sequences are amino acids\n");
- printf("-g --gop Gap opening costs\n");
- printf("-e --gep Gap extension costs\n");
- printf("-r --retree Number of reconstructions [default=0]\n");
- printf(" --tree_only only tree is produced\n");
- printf(" --eval_aln calculates only the sum-of-pairs-score of a given alignment\n");
- printf("-s --score calculates the sum of paris score after construction of an alignment. Can take a long time. [default: off]\n");
-// printf(" --make_ref_aln calculates the sum of paris score after construction of an alignment. Can take a long time. [default: off]\n");
- exit(0);
- }
- else
- {
- printf("Argument %s unknown\n", param);
- exit(1);
- }
- ++i;
- }
-}
-/******************************COPYRIGHT NOTICE*******************************/
-/*© Centro de Regulacio Genomica */
-/*and */
-/*Cedric Notredame */
-/*Fri Feb 18 08:27:45 CET 2011 - Revision 596. */
-/*All rights reserved.*/
-/*This file is part of T-COFFEE.*/
-/**/
-/* T-COFFEE is free software; you can redistribute it and/or modify*/
-/* it under the terms of the GNU General Public License as published by*/
-/* the Free Software Foundation; either version 2 of the License, or*/
-/* (at your option) any later version.*/
-/**/
-/* T-COFFEE is distributed in the hope that it will be useful,*/
-/* but WITHOUT ANY WARRANTY; without even the implied warranty of*/
-/* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the*/
-/* GNU General Public License for more details.*/
-/**/
-/* You should have received a copy of the GNU General Public License*/
-/* along with Foobar; if not, write to the Free Software*/
-/* Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA*/
-/*............................................... |*/
-/* If you need some more information*/
-/* cedric.notredame@europe.com*/
-/*............................................... |*/
-/**/
-/**/
-/* */
-/******************************COPYRIGHT NOTICE*******************************/
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