Exemple #1
0
static int gt_seqmutate_runner(int argc, const char **argv, int parsed_args,
                            void *tool_arguments, GtError *err)
{
  MutateArguments *arguments = tool_arguments;
  GtBioseqIterator *bsi;
  unsigned long i;
  GtBioseq *bioseq;
  GtSeq *mutated_seq;
  int had_err;

  gt_error_check(err);
  gt_assert(arguments);

  bsi = gt_bioseq_iterator_new(argc - parsed_args, argv + parsed_args);

  while (!(had_err = gt_bioseq_iterator_next(bsi, &bioseq, err)) && bioseq) {
    for (i = 0; i < gt_bioseq_number_of_sequences(bioseq); i++) {
      mutated_seq = gt_mutate_seq(gt_bioseq_get_description(bioseq, i),
                                  gt_bioseq_get_sequence(bioseq, i),
                                  gt_bioseq_get_sequence_length(bioseq, i),
                                  gt_bioseq_get_alphabet(bioseq),
                                  arguments->rate);
      gt_fasta_show_entry(gt_seq_get_description(mutated_seq),
                          gt_seq_get_orig(mutated_seq),
                          gt_seq_length(mutated_seq),
                          arguments->width, arguments->outfp);
      gt_seq_delete(mutated_seq);
    }
    gt_bioseq_delete(bioseq);
  }

  gt_bioseq_iterator_delete(bsi);

  return had_err;
}
Exemple #2
0
GtPBSResults* gt_pbs_find(const char *seq,
                          const char *rev_seq,
                          GtLTRElement *element,
                          GtPBSOptions *o,
                          GtError *err)
{
  GtSeq *seq_forward, *seq_rev;
  GtPBSResults *results;
  unsigned long j;
  GtAlignment *ali;
  GtAlphabet *a = gt_alphabet_new_dna();
  GtScoreFunction *sf = gt_dna_scorefunc_new(a,
                                             o->ali_score_match,
                                             o->ali_score_mismatch,
                                             o->ali_score_insertion,
                                             o->ali_score_deletion);

  gt_assert(seq && rev_seq && sf && a && element);

  results = gt_pbs_results_new(element, o);

  seq_forward = gt_seq_new(seq + (gt_ltrelement_leftltrlen(element))
                               - (o->radius),
                           2*o->radius + 1,
                           a);

  seq_rev     = gt_seq_new(rev_seq + (gt_ltrelement_rightltrlen(element))
                                   - (o->radius),
                           2*o->radius + 1,
                           a);

    for (j=0;j<gt_bioseq_number_of_sequences(o->trna_lib);j++)
  {
    GtSeq *trna_seq, *trna_from3;
    char *trna_from3_full;
    unsigned long trna_seqlen;

    trna_seq = gt_bioseq_get_seq(o->trna_lib, j);
    trna_seqlen = gt_seq_length(trna_seq);

    trna_from3_full = gt_calloc(trna_seqlen, sizeof (char));
    memcpy(trna_from3_full, gt_seq_get_orig(trna_seq),
           sizeof (char)*trna_seqlen);
    (void) gt_reverse_complement(trna_from3_full, trna_seqlen, err);
    trna_from3 = gt_seq_new_own(trna_from3_full, trna_seqlen, a);

    ali = gt_swalign(seq_forward, trna_from3, sf);
    gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
                   gt_seq_get_description(trna_seq), GT_STRAND_FORWARD,
                   results);
    gt_alignment_delete(ali);

    ali = gt_swalign(seq_rev, trna_from3, sf);
    gt_pbs_add_hit(results->hits, ali, o, trna_seqlen,
                   gt_seq_get_description(trna_seq), GT_STRAND_REVERSE,
                   results);
    gt_alignment_delete(ali);

    gt_seq_delete(trna_from3);
  }
  gt_seq_delete(seq_forward);
  gt_seq_delete(seq_rev);
  gt_score_function_delete(sf);
  gt_alphabet_delete(a);
  gt_array_sort(results->hits, gt_pbs_hit_compare);
  return results;
}