#include "genometools.h"

int main(int argc, const char *argv[])
{
  GtError *err;
  GtEncseq *es;
  GtEncseqLoader *el;
  GtEncseqReader *er;
  unsigned long i,
                tmp,
                desclen;
  const char *desc;
  char *buf;

  /* initialize GenomeTools library */
  gt_lib_init();

  /* create GtEncseqLoader */
  el = gt_encseq_loader_new();
  
  /* only accept indexes with description support */
  gt_encseq_loader_disable_autosupport(el);
  gt_encseq_loader_require_description_support(el);

  /* load the file */
  err = gt_error_new();  
  es = gt_encseq_loader_load(el, argv[1], err);
  gt_encseq_loader_delete(el);

  /* error checking */
  if (!es) {
    printf("%s", gt_error_get(err));
    exit(EXIT_FAILURE);
  }

  /* get number of sequences, e.g. 6 */
  tmp = gt_encseq_num_of_sequences(es);

  /* get total concatenated length, e.g. 156 */
  tmp = gt_encseq_total_length(es);

  /* get description */
  desc = gt_encseq_description(es, &desclen, 3);

  /* extend sequence by their virtual reverse complement */
  if (gt_alphabet_is_dna(gt_encseq_alphabet(es))) {
    gt_encseq_mirror(es, err);
  }

  /* get number of sequences, should now be 12 */
  tmp = gt_encseq_num_of_sequences(es);

  /* get total concatenated length, should now be 313 */
  tmp = gt_encseq_total_length(es);

  /* remove reverse complement */
  if (gt_encseq_is_mirrored(es))  
    gt_encseq_unmirror(es);

  /* get starting position of sequence 3 in the encoded sequence */
  tmp = gt_encseq_seqstartpos(es, 3);

  /* output sequence 3 as FASTA */
  printf(">%.*s\n", (int) desclen, desc);
  for (i = 0; i < gt_encseq_seqlength(es, 3); i++) {
    putc(gt_encseq_get_decoded_char(es, tmp + i,
                                    GT_READMODE_FORWARD), stdout);
  }
  printf("\n");

  /* alternative: using a reader */
  printf(">%.*s\n", (int) desclen, desc);
  er = gt_encseq_create_reader_with_readmode(es, GT_READMODE_FORWARD, tmp);
  for (i = 0; i < gt_encseq_seqlength(es, 3); i++) {
    putc(gt_encseq_reader_next_decoded_char(er), stdout);
  }
  gt_encseq_reader_delete(er);
  printf("\n");

  /* alternative: using a buffer (needs extra space) */
  printf(">%.*s\n", (int) desclen, desc);
  buf = calloc(gt_encseq_seqlength(es, 3) + 1, sizeof (char));
  gt_encseq_extract_decoded(es, buf, tmp, tmp + gt_encseq_seqlength(es, 3));
  printf("%s\n", buf);
  free(buf);

  /* cleanup */
  gt_error_delete(err);
  gt_encseq_delete(es);
  gt_lib_clean();
}

#!/usr/bin/env python
# -*- coding: utf-8 -*-

from gt.core.encseq import Encseq, EncseqLoader, EncseqReader
from gt.core.readmode import *
import sys

el = EncseqLoader()
es = el.load(sys.argv[1])

# get number of sequences, e.g. 6
tmp = es.num_of_sequences()

# get total concatenated length, e.g. 156
tmp = es.total_length()

# get description
desc = es.description(3)

# extend sequence by their virtual reverse complement
if es.alphabet().is_dna():
    es.mirror()

# get number of sequences, should now be 12
tmp = es.num_of_sequences()

# get total concatenated length, should now be 313
tmp = es.total_length()

# remove reverse complement
if es.is_mirrored():  
    es.unmirror()

# get starting position of sequence 3 in the encoded sequence
tmp = es.seqstartpos(3)

# output sequence 3 as FASTA
print(">%s" % desc)
for i in range(es.seqlength(3)):
    sys.stdout.write(es.get_decoded_char(tmp+i, FORWARD))
print

# alternative: using a reader
print(">%s" % desc)
er = es.create_reader_with_readmode(FORWARD, tmp)
for i in range(es.seqlength(3)):
    sys.stdout.write(er.next_decoded_char())
print

# alternative: using a buffer (needs extra space)
print(">%s" % desc)
buf = es.extract_decoded(tmp, tmp + es.seqlength(3))
print(buf)