static int md5_to_seqid(GtGenomeNode *gn, GtRegionMapping *region_mapping, GtError *err) { GtStr *seqid; int had_err = 0; gt_error_check(err); gt_assert(gn && region_mapping); seqid = gt_genome_node_get_seqid(gn); if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) { /* seqid is a MD5 seqid -> change id */ GtStr *desc = gt_str_new(); had_err = gt_region_mapping_get_description(region_mapping, desc, seqid, err); if (!had_err) { GtStr *new_seqid = gt_str_new(); gt_regular_seqid_save(new_seqid, desc); if (gt_feature_node_try_cast(gn)) { M2IChangeSeqidInfo info; info.new_seqid = new_seqid; info.region_mapping = region_mapping; had_err = gt_feature_node_traverse_children((GtFeatureNode*) gn, &info, m2i_change_seqid, true, err); } else gt_genome_node_change_seqid(gn, new_seqid); gt_str_delete(new_seqid); } gt_str_delete(desc); } return had_err; }
static int m2i_change_target_seqids(GtFeatureNode *fn, const char *target, GtRegionMapping *region_mapping, GtError *err) { GtStrArray *target_ids; GtArray *target_ranges, *target_strands; GtStr *desc, *new_seqid; unsigned long i; int had_err; gt_error_check(err); gt_assert(fn && target && region_mapping); target_ids = gt_str_array_new(); target_ranges = gt_array_new(sizeof (GtRange)); target_strands = gt_array_new(sizeof (GtStrand)); desc = gt_str_new(); new_seqid = gt_str_new(); had_err = gt_gff3_parser_parse_all_target_attributes(target, false, target_ids, target_ranges, target_strands, "", 0, err); for (i = 0; !had_err && i < gt_str_array_size(target_ids); i++) { GtStr *seqid; gt_str_reset(desc); gt_str_reset(new_seqid); seqid = gt_str_array_get_str(target_ids, i); had_err = gt_region_mapping_get_description(region_mapping, desc, seqid, err); if (!had_err) gt_regular_seqid_save(new_seqid, desc); gt_str_array_set(target_ids, i, new_seqid); } if (!had_err) { GtStr *new_target = gt_str_new(); gt_gff3_parser_build_target_str(new_target, target_ids, target_ranges, target_strands); gt_feature_node_set_attribute(fn, GT_GFF_TARGET, gt_str_get(new_target)); gt_str_delete(new_target); } gt_str_delete(new_seqid); gt_str_delete(desc); gt_array_delete(target_strands); gt_array_delete(target_ranges); gt_str_array_delete(target_ids); return had_err; }
int gt_ltrfileout_stream_next(GtNodeStream *ns, GtGenomeNode **gn, GtError *err) { GtLTRdigestFileOutStream *ls; GtFeatureNode *fn; GtRange lltr_rng = {GT_UNDEF_UWORD, GT_UNDEF_UWORD}, rltr_rng = {GT_UNDEF_UWORD, GT_UNDEF_UWORD}, ppt_rng = {GT_UNDEF_UWORD, GT_UNDEF_UWORD}, pbs_rng = {GT_UNDEF_UWORD, GT_UNDEF_UWORD}; int had_err; GtUword i=0; gt_error_check(err); ls = gt_ltrdigest_file_out_stream_cast(ns); /* initialize this element */ memset(&ls->element, 0, sizeof (GtLTRElement)); /* get annotations from parser */ had_err = gt_node_stream_next(ls->in_stream, gn, err); if (!had_err && *gn) { GtFeatureNodeIterator* gni; GtFeatureNode *mygn; /* only process feature nodes */ if (!(fn = gt_feature_node_try_cast(*gn))) return 0; ls->element.pdomorder = gt_array_new(sizeof (const char*)); /* fill LTRElement structure from GFF3 subgraph */ gni = gt_feature_node_iterator_new(fn); for (mygn = fn; mygn != NULL; mygn = gt_feature_node_iterator_next(gni)) (void) gt_genome_node_accept((GtGenomeNode*) mygn, (GtNodeVisitor*) ls->lv, err); gt_feature_node_iterator_delete(gni); } if (!had_err && ls->element.mainnode != NULL) { char desc[GT_MAXFASTAHEADER]; GtFeatureNode *ltr3, *ltr5; GtStr *sdesc, *sreg, *seq; /* find sequence in GtEncseq */ sreg = gt_genome_node_get_seqid((GtGenomeNode*) ls->element.mainnode); sdesc = gt_str_new(); had_err = gt_region_mapping_get_description(ls->rmap, sdesc, sreg, err); if (!had_err) { GtRange rng; ls->element.seqid = gt_calloc((size_t) ls->seqnamelen+1, sizeof (char)); (void) snprintf(ls->element.seqid, MIN((size_t) gt_str_length(sdesc), (size_t) ls->seqnamelen)+1, "%s", gt_str_get(sdesc)); gt_cstr_rep(ls->element.seqid, ' ', '_'); if (gt_str_length(sdesc) > (GtUword) ls->seqnamelen) ls->element.seqid[ls->seqnamelen] = '\0'; (void) gt_ltrelement_format_description(&ls->element, ls->seqnamelen, desc, (size_t) (GT_MAXFASTAHEADER-1)); gt_str_delete(sdesc); /* output basic retrotransposon data */ lltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftLTR); rltr_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightLTR); rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.mainnode); gt_file_xprintf(ls->tabout_file, GT_WU"\t"GT_WU"\t"GT_WU"\t%s\t"GT_WU"\t"GT_WU"\t"GT_WU"\t" GT_WU"\t"GT_WU"\t"GT_WU"\t", rng.start, rng.end, gt_ltrelement_length(&ls->element), ls->element.seqid, lltr_rng.start, lltr_rng.end, gt_ltrelement_leftltrlen(&ls->element), rltr_rng.start, rltr_rng.end, gt_ltrelement_rightltrlen(&ls->element)); } seq = gt_str_new(); /* output TSDs */ if (!had_err && ls->element.leftTSD != NULL) { GtRange tsd_rng; tsd_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.leftTSD); had_err = gt_extract_feature_sequence(seq, (GtGenomeNode*) ls->element.leftTSD, gt_symbol(gt_ft_target_site_duplication), false, NULL, NULL, ls->rmap, err); if (!had_err) { gt_file_xprintf(ls->tabout_file, ""GT_WU"\t"GT_WU"\t%s\t", tsd_rng.start, tsd_rng.end, gt_str_get(seq)); } gt_str_reset(seq); } else gt_file_xprintf(ls->tabout_file, "\t\t\t"); if (!had_err && ls->element.rightTSD != NULL) { GtRange tsd_rng; tsd_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.rightTSD); had_err = gt_extract_feature_sequence(seq, (GtGenomeNode*) ls->element.rightTSD, gt_symbol(gt_ft_target_site_duplication), false, NULL, NULL, ls->rmap, err); if (!had_err) { gt_file_xprintf(ls->tabout_file, ""GT_WU"\t"GT_WU"\t%s\t", tsd_rng.start, tsd_rng.end, gt_str_get(seq)); } gt_str_reset(seq); } else gt_file_xprintf(ls->tabout_file, "\t\t\t"); /* output PPT */ if (!had_err && ls->element.ppt != NULL) { GtStrand ppt_strand = gt_feature_node_get_strand(ls->element.ppt); ppt_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.ppt); had_err = gt_extract_feature_sequence(seq, (GtGenomeNode*) ls->element.ppt, gt_symbol(gt_ft_RR_tract), false, NULL, NULL, ls->rmap, err); if (!had_err) { gt_fasta_show_entry(desc, gt_str_get(seq), gt_range_length(&ppt_rng), GT_FSWIDTH, ls->pptout_file); gt_file_xprintf(ls->tabout_file, ""GT_WU"\t"GT_WU"\t%s\t%c\t%d\t", ppt_rng.start, ppt_rng.end, gt_str_get(seq), GT_STRAND_CHARS[ppt_strand], (ppt_strand == GT_STRAND_FORWARD ? abs((int) (rltr_rng.start - ppt_rng.end)) : abs((int) (lltr_rng.end - ppt_rng.start)))); } gt_str_reset(seq); } else gt_file_xprintf(ls->tabout_file, "\t\t\t\t\t"); /* output PBS */ if (!had_err && ls->element.pbs != NULL) { GtStrand pbs_strand; pbs_strand = gt_feature_node_get_strand(ls->element.pbs); pbs_rng = gt_genome_node_get_range((GtGenomeNode*) ls->element.pbs); had_err = gt_extract_feature_sequence(seq, (GtGenomeNode*) ls->element.pbs, gt_symbol(gt_ft_primer_binding_site), false, NULL, NULL, ls->rmap, err); if (!had_err) { gt_fasta_show_entry(desc, gt_str_get(seq), gt_range_length(&pbs_rng), GT_FSWIDTH, ls->pbsout_file); gt_file_xprintf(ls->tabout_file, ""GT_WU"\t"GT_WU"\t%c\t%s\t%s\t%s\t%s\t%s\t", pbs_rng.start, pbs_rng.end, GT_STRAND_CHARS[pbs_strand], gt_feature_node_get_attribute(ls->element.pbs, "trna"), gt_str_get(seq), gt_feature_node_get_attribute(ls->element.pbs, "pbsoffset"), gt_feature_node_get_attribute(ls->element.pbs, "trnaoffset"), gt_feature_node_get_attribute(ls->element.pbs, "edist")); } gt_str_reset(seq); } else gt_file_xprintf(ls->tabout_file, "\t\t\t\t\t\t\t\t"); /* output protein domains */ if (!had_err && ls->element.pdoms != NULL) { GtStr *pdomorderstr = gt_str_new(); for (i=0; !had_err && i<gt_array_size(ls->element.pdomorder); i++) { const char* key = *(const char**) gt_array_get(ls->element.pdomorder, i); GtArray *entry = (GtArray*) gt_hashmap_get(ls->element.pdoms, key); had_err = write_pdom(ls, entry, key, ls->rmap, desc, err); } if (GT_STRAND_REVERSE == gt_feature_node_get_strand(ls->element.mainnode)) gt_array_reverse(ls->element.pdomorder); for (i=0 ;!had_err && i<gt_array_size(ls->element.pdomorder); i++) { const char* name = *(const char**) gt_array_get(ls->element.pdomorder, i); gt_str_append_cstr(pdomorderstr, name); if (i != gt_array_size(ls->element.pdomorder)-1) gt_str_append_cstr(pdomorderstr, "/"); } gt_file_xprintf(ls->tabout_file, "%s", gt_str_get(pdomorderstr)); gt_str_delete(pdomorderstr); } /* output LTRs (we just expect them to exist) */ switch (gt_feature_node_get_strand(ls->element.mainnode)) { case GT_STRAND_REVERSE: ltr5 = ls->element.rightLTR; ltr3 = ls->element.leftLTR; break; case GT_STRAND_FORWARD: default: ltr5 = ls->element.leftLTR; ltr3 = ls->element.rightLTR; break; } if (!had_err) { had_err = gt_extract_feature_sequence(seq, (GtGenomeNode*) ltr5, gt_symbol(gt_ft_long_terminal_repeat), false, NULL, NULL, ls->rmap, err); } if (!had_err) { gt_fasta_show_entry(desc, gt_str_get(seq), gt_str_length(seq), GT_FSWIDTH, ls->ltr5out_file); gt_str_reset(seq); } if (!had_err) { had_err = gt_extract_feature_sequence(seq, (GtGenomeNode*) ltr3, gt_symbol(gt_ft_long_terminal_repeat), false, NULL, NULL, ls->rmap, err); } if (!had_err) { gt_fasta_show_entry(desc, gt_str_get(seq), gt_str_length(seq), GT_FSWIDTH, ls->ltr3out_file); gt_str_reset(seq); } /* output complete oriented element */ if (!had_err) { had_err = gt_extract_feature_sequence(seq, (GtGenomeNode*) ls->element.mainnode, gt_symbol(gt_ft_LTR_retrotransposon), false, NULL, NULL, ls->rmap, err); } if (!had_err) { gt_fasta_show_entry(desc,gt_str_get(seq), gt_str_length(seq), GT_FSWIDTH, ls->elemout_file); gt_str_reset(seq); } gt_file_xprintf(ls->tabout_file, "\n"); gt_str_delete(seq); } gt_hashmap_delete(ls->element.pdoms); gt_array_delete(ls->element.pdomorder); gt_free(ls->element.seqid); return had_err; }