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fasta_nucleotide_changer.c

/*
    FASTX-toolkit - FASTA/FASTQ preprocessing tools.
    Copyright (C) 2009  A. Gordon (gordon@cshl.edu)

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU Affero General Public License as
    published by the Free Software Foundation, either version 3 of the
    License, or (at your option) any later version.

    This program 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 Affero General Public License for more details.

    You should have received a copy of the GNU Affero General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.
*/
#include <limits.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <getopt.h>
#include <errno.h>
#include <err.h>

#include <config.h>

#include "fastx.h"
#include "fastx_args.h"

#define MAX_ADAPTER_LEN 100

const char* usage=
"usage: fasta_nucleotide_changer [-h] [-z] [-v] [-i INFILE] [-o OUTFILE] [-r] [-d]\n" \
"Part of " PACKAGE_STRING " by A. Gordon (gordon@cshl.edu)\n" \
"\n" \
"   [-h]         = This helpful help screen.\n" \
"   [-z]         = Compress output with GZIP.\n" \
"   [-v]         = Verbose mode. Prints a short summary.\n" \
"                  with [-o], summary is printed to STDOUT.\n" \
"                  Otherwise, summary is printed to STDERR.\n" \
"   [-i INFILE]  = FASTA/Q input file. default is STDIN.\n" \
"   [-o OUTFILE] = FASTA/Q output file. default is STDOUT.\n" \
"   [-r]         = DNA-to-RNA mode - change T's into U's.\n" \
"   [-d]         = RNA-to-DNA mode - change U's into T's.\n" \
"\n";

int flag_dna_mode = 0;
int flag_rna_mode = 0;

FASTX fastx;

int parse_program_args(int __attribute__((unused)) optind, int optc, char __attribute__((unused))* optarg)
{
      switch(optc) {
      case 'd':
            flag_dna_mode = 1 ;
            break;

      case 'r':
            flag_rna_mode = 1 ;
            break;

      default:
            errx(1, __FILE__ ":%d: Unknown argument (%c)", __LINE__, optc ) ;
      }
      return 1;
}


int main(int argc, char* argv[])
{
      size_t i;
      char nuc_from ;
      char nuc_to;
      size_t changes_count=0 ;
      
      fastx_parse_cmdline(argc, argv, "rd", parse_program_args);

      if ( !flag_dna_mode && !flag_rna_mode )
            errx(1,"Please specify either RNA mode (-r) or DNA mode (-d)" );

      if ( flag_dna_mode && flag_rna_mode )
            errx(1,"RNA mode (-r) and DNA mode (-d) can not be used together." );

      if ( flag_dna_mode ) {
            nuc_from = 'U';
            nuc_to   = 'T';
      }
      if ( flag_rna_mode ) {
            nuc_from = 'T';
            nuc_to   = 'U';
      }

      fastx_init_reader(&fastx, get_input_filename(), 
            FASTA_OR_FASTQ, ALLOW_N | ALLOW_U, REQUIRE_UPPERCASE,
            get_fastq_ascii_quality_offset() );

      fastx_init_writer(&fastx, get_output_filename(), OUTPUT_FASTA, compress_output_flag());

      while ( fastx_read_next_record(&fastx) ) {

            for (i=0; i < strlen(fastx.nucleotides) ; i++)  {
                  if ( fastx.nucleotides[i] == nuc_to ) {
                        errx(1,"Error: found '%c' nucleotide on line %lld. (input should not contain '%c' nucleotides in %s mode)",
                              nuc_to, fastx.input_line_number, nuc_to,(flag_dna_mode)?"RNA-to-DNA":"DNA-to-RNA" );
                  }
                  if ( fastx.nucleotides[i] == nuc_from ) {
                        fastx.nucleotides[i] = nuc_to ;
                        changes_count++;
                  }
            }
            
            fastx_write_record(&fastx);
      }

      if ( verbose_flag() ) {
            fprintf(get_report_file(), "Mode: %s\n", (flag_dna_mode)?"RNA-to-DNA":"DNA-to-RNA" ) ;
            fprintf(get_report_file(), "Input: %zu reads.\n", num_input_reads(&fastx) ) ;
            fprintf(get_report_file(), "Output: %zu reads.\n", num_output_reads(&fastx) ) ;
            fprintf(get_report_file(), "Nucleotides changed: %zu\n", changes_count ) ;
      }
      return 0;
}

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