vsearch-2.17.1/src/fasta.cc

/*

  VSEARCH: a versatile open source tool for metagenomics

  Copyright (C) 2014-2021, Torbjorn Rognes, Frederic Mahe and Tomas Flouri
  All rights reserved.

  Contact: Torbjorn Rognes <torognes@ifi.uio.no>,
  Department of Informatics, University of Oslo,
  PO Box 1080 Blindern, NO-0316 Oslo, Norway

  This software is dual-licensed and available under a choice
  of one of two licenses, either under the terms of the GNU
  General Public License version 3 or the BSD 2-Clause License.


  GNU General Public License version 3

  This program 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 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 General Public License for more details.

  You should have received a copy of the GNU General Public License
  along with this program.  If not, see <http://www.gnu.org/licenses/>.


  The BSD 2-Clause License

  Redistribution and use in source and binary forms, with or without
  modification, are permitted provided that the following conditions
  are met:

  1. Redistributions of source code must retain the above copyright
  notice, this list of conditions and the following disclaimer.

  2. 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.

  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 HOLDER 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.

*/

#include "vsearch.h"

fastx_handle fasta_open(const char * filename)
{
  fastx_handle h = fastx_open(filename);

  if (fastx_is_fastq(h) && ! h->is_empty) {
    fatal("FASTA file expected, FASTQ file found (%s)", filename);

        }

  return h;
}

void fasta_close(fastx_handle h)
{
  fastx_close(h);
}

void fasta_filter_sequence(fastx_handle h,
                           unsigned int * char_action,
                           const unsigned char * char_mapping)
{
  /* Strip unwanted characters from the sequence and raise warnings or
     errors on certain characters. */

  char * p = h->sequence_buffer.data;
  char * q = p;
  char c;
  char msg[200];

  while ((c = *p++))
    {
      char m = char_action[(unsigned char)c];

      switch(m)
        {
        case 0:
          /* stripped */
          h->stripped_all++;
          h->stripped[(unsigned char)c]++;
          break;

        case 1:
          /* legal character */
          *q++ = char_mapping[(unsigned char)(c)];
          break;

        case 2:
          /* fatal character */
          if ((c>=32) && (c<127)) {
            snprintf(msg,
                     200,
                     "Illegal character '%c' in sequence on line %" PRIu64 " of FASTA file",
                     (unsigned char)c,
                     h->lineno);
          } else {
            snprintf(msg,
                     200,
                     "Illegal unprintable ASCII character no %d in sequence on line %" PRIu64 " of FASTA file",
                     (unsigned char) c,
                     h->lineno);

        }
          fatal(msg);
          break;

        case 3:
          /* silently stripped chars (whitespace) */
          break;

        case 4:
          /* newline (silently stripped) */
          h->lineno++;
          break;
        }
    }

  /* add zero after sequence */
  *q = 0;
  h->sequence_buffer.length = q - h->sequence_buffer.data;
}

bool fasta_next(fastx_handle h,
                bool truncateatspace,
                const unsigned char * char_mapping)
{
  h->lineno_start = h->lineno;

  h->header_buffer.length = 0;
  h->header_buffer.data[0] = 0;
  h->sequence_buffer.length = 0;
  h->sequence_buffer.data[0] = 0;

  uint64_t rest = fastx_file_fill_buffer(h);

  if (rest == 0) {
    return false;

        }

  /* read header */

  /* check initial > character */

  if (h->file_buffer.data[h->file_buffer.position] != '>')
    {
      fprintf(stderr, "Found character %02x\n", (unsigned char)(h->file_buffer.data[h->file_buffer.position]));
      fatal("Invalid FASTA - header must start with > character");
    }
  h->file_buffer.position++;
  rest--;

  char * lf = nullptr;
  while (lf == nullptr)
    {
      /* get more data if buffer empty*/
      rest = fastx_file_fill_buffer(h);
      if (rest == 0) {
        fatal("Invalid FASTA - header must be terminated with newline");

        }

      /* find LF */
      lf = (char *) memchr(h->file_buffer.data + h->file_buffer.position,
                           '\n',
                           rest);

      /* copy to header buffer */
      uint64_t len = rest;
      if (lf)
        {
          /* LF found, copy up to and including LF */
          len = lf - (h->file_buffer.data + h->file_buffer.position) + 1;
          h->lineno++;
        }
      buffer_extend(& h->header_buffer,
                    h->file_buffer.data + h->file_buffer.position,
                    len);
      h->file_buffer.position += len;
      rest -= len;
    }

  /* read one or more sequence lines */

  while (true)
    {
      /* get more data, if necessary */
      rest = fastx_file_fill_buffer(h);

      /* end if no more data */
      if (rest == 0) {
        break;

        }

      /* end if new sequence starts */
      if (lf && (h->file_buffer.data[h->file_buffer.position] == '>')) {
        break;

        }

      /* find LF */
      lf = (char *) memchr(h->file_buffer.data + h->file_buffer.position,
                           '\n', rest);

      uint64_t len = rest;
      if (lf)
        {
          /* LF found, copy up to and including LF */
          len = lf - (h->file_buffer.data + h->file_buffer.position) + 1;
        }
      buffer_extend(& h->sequence_buffer,
                    h->file_buffer.data + h->file_buffer.position,
                    len);
      h->file_buffer.position += len;
      rest -= len;
    }

  h->seqno++;

  fastx_filter_header(h, truncateatspace);
  fasta_filter_sequence(h, char_fasta_action, char_mapping);

  return true;
}

int64_t fasta_get_abundance(fastx_handle h)
{
  // return 1 if not present
  int64_t size = header_get_size(h->header_buffer.data,
                                 h->header_buffer.length);
  if (size > 0) {
    return size;
  } else {
    return 1;

        }
}

int64_t fasta_get_abundance_and_presence(fastx_handle h)
{
  // return 0 if not present
  return header_get_size(h->header_buffer.data, h->header_buffer.length);
}

uint64_t fasta_get_position(fastx_handle h)
{
  return h->file_position;
}

uint64_t fasta_get_size(fastx_handle h)
{
  return h->file_size;
}

uint64_t fasta_get_lineno(fastx_handle h)
{
  return h->lineno_start;
}

uint64_t fasta_get_seqno(fastx_handle h)
{
  return h->seqno;
}

uint64_t fasta_get_header_length(fastx_handle h)
{
  return h->header_buffer.length;
}

uint64_t fasta_get_sequence_length(fastx_handle h)
{
  return h->sequence_buffer.length;
}

char * fasta_get_header(fastx_handle h)
{
  return h->header_buffer.data;
}

char * fasta_get_sequence(fastx_handle h)
{
  return h->sequence_buffer.data;
}


/* fasta output */

void fasta_print_sequence(FILE * fp, char * seq, uint64_t len, int width)
{
  /*
     The actual length of the sequence may be longer than "len", but only
     "len" characters are printed.

     Specify width of lines - zero (or <1) means linearize (all on one line).
  */

  if (width < 1) {
    fprintf(fp, "%.*s\n", (int)(len), seq);
  } else
    {
      int64_t rest = len;
      for(uint64_t i=0; i<len; i += width)
        {
          fprintf(fp, "%.*s\n", (int)(MIN(rest,width)), seq+i);
          rest -= width;
        }
    }
}

void fasta_print(FILE * fp, const char * hdr,
                 char * seq, uint64_t len)
{
  fprintf(fp, ">%s\n", hdr);
  fasta_print_sequence(fp, seq, len, opt_fasta_width);
}

inline void fprint_seq_label(FILE * fp, char * seq, int len)
{
  /* normalize first? */
  fprintf(fp, "%.*s", len, seq);
}

void fasta_print_general(FILE * fp,
                         const char * prefix,
                         char * seq,
                         int len,
                         char * header,
                         int header_len,
                         unsigned int abundance,
                         int ordinal,
                         double ee,
                         int clustersize,
                         int clusterid,
                         const char * score_name,
                         double score)
{
  fprintf(fp, ">");

  if (prefix) {
    fprintf(fp, "%s", prefix);

        }

  if (opt_relabel_self) {
    fprint_seq_label(fp, seq, len);
  } else if (opt_relabel_sha1) {
    fprint_seq_digest_sha1(fp, seq, len);
  } else if (opt_relabel_md5) {
    fprint_seq_digest_md5(fp, seq, len);
  } else if (opt_relabel && (ordinal > 0)) {
    fprintf(fp, "%s%d", opt_relabel, ordinal);
  } else
    {
      bool xsize = opt_xsize || (opt_sizeout && (abundance > 0));
      bool xee = opt_xee || ((opt_eeout || opt_fastq_eeout) && (ee >= 0.0));
      header_fprint_strip_size_ee(fp,
                                  header,
                                  header_len,
                                  xsize,
                                  xee);
    }

  if (opt_label_suffix) {
    fprintf(fp, "%s", opt_label_suffix);

        }

  if (clustersize > 0) {
    fprintf(fp, ";seqs=%d", clustersize);

        }

  if (clusterid >= 0) {
    fprintf(fp, ";clusterid=%d", clusterid);

        }

  if (opt_sizeout && (abundance > 0)) {
    fprintf(fp, ";size=%u", abundance);

        }

  if ((opt_eeout || opt_fastq_eeout) && (ee >= 0.0)) {
    fprintf(fp, ";ee=%.4lf", ee);

        }

  if (score_name) {
    fprintf(fp, ";%s=%.4lf", score_name, score);

        }

  if (opt_relabel_keep &&
      ((opt_relabel && (ordinal > 0)) || opt_relabel_sha1 || opt_relabel_md5 || opt_relabel_self)) {
    fprintf(fp, " %s", header);

        }

  fprintf(fp, "\n");

  if (seq) {
    fasta_print_sequence(fp, seq, len, opt_fasta_width);

        }
}

void fasta_print_db_relabel(FILE * fp,
                            uint64_t seqno,
                            int ordinal)
{
  fasta_print_general(fp,
                      nullptr,
                      db_getsequence(seqno),
                      db_getsequencelen(seqno),
                      db_getheader(seqno),
                      db_getheaderlen(seqno),
                      db_getabundance(seqno),
                      ordinal,
                      -1.0,
                      -1, -1,
                      nullptr, 0.0);
}

void fasta_print_db(FILE * fp, uint64_t seqno)
{
  fasta_print_general(fp,
                      nullptr,
                      db_getsequence(seqno),
                      db_getsequencelen(seqno),
                      db_getheader(seqno),
                      db_getheaderlen(seqno),
                      db_getabundance(seqno),
                      0,
                      -1.0,
                      -1, -1,
                      nullptr, 0.0);
}