text: /*
    Copyright (c) 2003-2010 Gordon Gremme <gordon@gremme.org>
    Copyright (c) 2003-2008 Center for Bioinformatics, University of Hamburg
  
    Permission to use, copy, modify, and distribute this software for any
    purpose with or without fee is hereby granted, provided that the above
    copyright notice and this permission notice appear in all copies.
  
    THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
    WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
    MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
    ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
    WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
    ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
    OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
  */
  
  #include "core/bioseq.h"
  #include "core/compat.h"
  #include "core/fa.h"
  #include "core/fasta.h"
  #include "core/fileutils_api.h"
  #include "core/ma.h"
  #include "core/option_api.h"
  #include "core/output_file.h"
  #include "core/unused_api.h"
  #include "core/xansi_api.h"
  #include "tools/gt_splitfasta.h"
  
  typedef struct {
    GtUword max_filesize_in_MB, width;
    unsigned int num_files;
    GtStr *splitdesc;
    bool force;
  } SplitfastaArguments;
  
  static void* gt_splitfasta_arguments_new(void)
  {
    SplitfastaArguments *arguments = gt_calloc(1, sizeof *arguments);
    arguments->splitdesc = gt_str_new();
    return arguments;
  }
  
  void gt_splitfasta_arguments_delete(void *tool_arguments)
  {
    SplitfastaArguments *arguments = tool_arguments;
    if (!arguments) return;
    gt_str_delete(arguments->splitdesc);
    gt_free(arguments);
  }
  
  static GtOptionParser* gt_splitfasta_option_parser_new(void *tool_arguments)
  {
    SplitfastaArguments *arguments = tool_arguments;
    GtOptionParser *op;
    GtOption *targetsize_option, *splitdesc_option, *o, *numfiles_option;
    gt_assert(arguments);
    op = gt_option_parser_new("[option ...] fastafile","Split the supplied fasta "
                           "file.");
  
    numfiles_option = gt_option_new_uint_min("numfiles",
                                             "set the number of target files "
                                             "",
                                             &arguments->num_files, 0,
                                             1);
    gt_option_parser_add_option(op, numfiles_option);
  
    targetsize_option = gt_option_new_uword_min("targetsize",
                                                "set the target file "
                                                "size in MB",
                                                &arguments->max_filesize_in_MB,
                                                50, 1);
    gt_option_parser_add_option(op, targetsize_option);
    splitdesc_option = gt_option_new_string("splitdesc",
                                            "put every fasta entry in "
                                            "a separate file named by its "
                                            "description in the given directory",
                                            arguments->splitdesc, NULL);
    gt_option_parser_add_option(op, splitdesc_option);
    gt_option_exclude(targetsize_option, splitdesc_option);
    gt_option_exclude(numfiles_option, splitdesc_option);
    gt_option_exclude(numfiles_option, targetsize_option);
    o = gt_option_new_width(&arguments->width);
    gt_option_parser_add_option(op, o);
    o = gt_option_new_bool(GT_FORCE_OPT_CSTR, "force writing to output file",
                           &arguments->force, false);
    gt_option_parser_add_option(op, o);
    gt_option_parser_set_min_max_args(op, 1, 1);
    return op;
  }
  
  static GtUword buf_contains_separator(char *buf, int offset,
                                              int read_bytes)
  {
    char *cc;
    gt_assert(buf && offset < read_bytes);
    for (cc = buf + offset; cc < buf + read_bytes; cc++) {
      if (*cc == '>')
        return cc - buf + 1;
    }
    return 0;
  }
  
  static int split_description(const char *filename, GtStr *splitdesc,
                               GtUword width, bool force, GtError *err)
  {
    GtUword i;
    GtBioseq *bioseq;
    GtStr *descname;
    int had_err = 0;
    gt_error_check(err);
    gt_assert(filename && splitdesc && gt_str_length(splitdesc));
  
    descname = gt_str_new();
    if (!(bioseq = gt_bioseq_new(filename, err)))
      had_err = -1;
  
    for (i = 0; !had_err && i < gt_bioseq_number_of_sequences(bioseq); i++) {
      GtFile *outfp;
      char *seq;
      gt_str_reset(descname);
      gt_str_append_str(descname, splitdesc);
      gt_str_append_char(descname, GT_PATH_SEPARATOR);
      gt_str_append_cstr(descname, gt_bioseq_get_description(bioseq, i));
      gt_str_append_cstr(descname, gt_file_suffix(filename));
      if (!(outfp = gt_output_file_xopen_forcecheck(gt_str_get(descname), "w",
                                                   force, err))) {
        had_err = -1;
        break;
      }
      seq = gt_bioseq_get_sequence(bioseq, i);
      gt_fasta_show_entry(gt_bioseq_get_description(bioseq, i), seq,
                          gt_bioseq_get_sequence_length(bioseq, i), width,
                          outfp);
      gt_free(seq);
      gt_file_delete(outfp);
    }
  
    gt_bioseq_delete(bioseq);
    gt_str_delete(descname);
  
    return had_err;
  }
  
  static int split_fasta_file(const char *filename, GtUword max_filesize,
                              bool force, GtError *err)
  {
    GtFile *srcfp = NULL, *destfp = NULL;
    GtStr *destfilename = NULL;
    GtUword filenum = 0, bytecount = 0, separator_pos;
    int read_bytes, had_err = 0;
    char buf[BUFSIZ];
  
    gt_error_check(err);
    gt_assert(filename && max_filesize);
  
    /* open source file */
    srcfp = gt_file_xopen(filename, "r");
    gt_assert(srcfp);
  
    /* read start characters */
    if ((read_bytes = gt_file_xread(srcfp, buf, BUFSIZ)) == 0) {
      gt_error_set(err, "file \"%s\" is empty", filename);
      had_err = -1;
    }
    bytecount += read_bytes;
  
    /* make sure the file is in fasta format */
    if (!had_err && buf[0] != '>') {
      gt_error_set(err, "file is not in FASTA format");
      had_err = -1;
    }
  
    if (!had_err) {
      /* open destination file */
      destfilename = gt_str_new();
      gt_str_append_cstr_nt(destfilename, filename,
                            gt_file_basename_length(filename));
      gt_str_append_char(destfilename, '.');
      gt_str_append_ulong(destfilename, ++filenum);
      gt_str_append_cstr(destfilename,
                         gt_file_mode_suffix(gt_file_mode(srcfp)));
      if (!(destfp = gt_output_file_xopen_forcecheck(gt_str_get(destfilename),
                                                    "w",
                                                    force, err))) {
        had_err = -1;
      }
      if (!had_err)
        gt_file_xwrite(destfp, buf, read_bytes);
  
      while (!had_err &&
             (read_bytes = gt_file_xread(srcfp, buf, BUFSIZ)) != 0) {
        if (bytecount + read_bytes > max_filesize) {
          int offset = bytecount < max_filesize ? max_filesize - bytecount : 0;
          if ((separator_pos = buf_contains_separator(buf, offset, read_bytes))) {
            separator_pos--;
            gt_assert(separator_pos < read_bytes);
            if (separator_pos)
              gt_file_xwrite(destfp, buf, separator_pos);
            /* close current file */
            gt_file_delete(destfp);
            /* open new file */
            gt_str_reset(destfilename);
            gt_str_append_cstr_nt(destfilename, filename,
                                  gt_file_basename_length(filename));
            gt_str_append_char(destfilename, '.');
            gt_str_append_ulong(destfilename, ++filenum);
            gt_str_append_cstr(destfilename,
                               gt_file_mode_suffix(gt_file_mode(srcfp)));
            if (!(destfp =
                    gt_output_file_xopen_forcecheck(gt_str_get(destfilename), "w",
                                                   force, err))) {
              had_err = -1;
              break;
            }
            bytecount = read_bytes - separator_pos; /* reset */
            gt_assert(buf[separator_pos] == '>');
            gt_file_xwrite(destfp, buf + separator_pos,
                           read_bytes - separator_pos);
            continue;
          }
        }
        bytecount += read_bytes;
        gt_file_xwrite(destfp, buf, read_bytes);
      }
    }
  
    /* free */
    gt_str_delete(destfilename);
  
    /* close current file */
    gt_file_delete(destfp);
  
    /* close source file */
    gt_file_delete(srcfp);
  
    return had_err;
  }
  
  static int gt_splitfasta_runner(GT_UNUSED int argc, const char **argv,
                                  int parsed_args, void *tool_arguments,
                                  GtError *err)
  {
    SplitfastaArguments *arguments = tool_arguments;
    unsigned int num_files;
    int had_err;
    off_t file_size;
    const char* filename;
    gt_error_check(err);
    gt_assert(arguments);
  
    num_files = arguments->num_files;
    filename = argv[parsed_args];
  
    if (gt_str_length(arguments->splitdesc)) {
      had_err = split_description(filename, arguments->splitdesc,
                                  arguments->width, arguments->force, err);
    }
    else {
      GtUword max_filesize;
      if (num_files) {
        /* set the maxfile size based on requested number of files */
        file_size = gt_file_estimate_size(filename);
        max_filesize= file_size / num_files ;
      }
      else
        max_filesize= arguments->max_filesize_in_MB << 20;
      had_err = split_fasta_file(filename, max_filesize, arguments->force, err);
    }
  
    return had_err;
  }
  
  GtTool* gt_splitfasta(void)
  {
    return gt_tool_new(gt_splitfasta_arguments_new,
                       gt_splitfasta_arguments_delete,
                       gt_splitfasta_option_parser_new,
                       NULL,
                       gt_splitfasta_runner);
  }
  