GtFeatureIndex *agn_import_simple(int numfiles, const char **filenames,
char *type, AgnLogger *logger)
{
GtFeatureIndex *features = gt_feature_index_memory_new();
GtNodeStream *gff3 = gt_gff3_in_stream_new_unsorted(numfiles, filenames);
gt_gff3_in_stream_check_id_attributes((GtGFF3InStream *)gff3);
gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream *)gff3);
GtHashmap *typestokeep = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
gt_hashmap_add(typestokeep, type, type);
GtNodeStream *filterstream = agn_filter_stream_new(gff3, typestokeep);
GtNodeStream *featstream = gt_feature_out_stream_new(filterstream, features);
GtError *error = gt_error_new();
int result = gt_node_stream_pull(featstream, error);
if(result == -1)
{
agn_logger_log_error(logger, "error processing node stream: %s",
gt_error_get(error));
}
gt_error_delete(error);
if(agn_logger_has_error(logger))
{
gt_feature_index_delete(features);
features = NULL;
}
gt_node_stream_delete(gff3);
gt_node_stream_delete(filterstream);
gt_node_stream_delete(featstream);
return features;
}
GtFeatureIndex *agn_import_canonical(int numfiles, const char **filenames,
AgnLogger *logger)
{
GtNodeStream *gff3 = gt_gff3_in_stream_new_unsorted(numfiles, filenames);
gt_gff3_in_stream_check_id_attributes((GtGFF3InStream *)gff3);
gt_gff3_in_stream_enable_tidy_mode((GtGFF3InStream *)gff3);
GtFeatureIndex *features = gt_feature_index_memory_new();
GtNodeStream *cgstream = agn_canon_gene_stream_new(gff3, logger);
GtNodeStream *featstream = gt_feature_out_stream_new(cgstream, features);
GtError *error = gt_error_new();
int result = gt_node_stream_pull(featstream, error);
if(result == -1)
{
agn_logger_log_error(logger, "error processing node stream: %s",
gt_error_get(error));
}
gt_error_delete(error);
if(agn_logger_has_error(logger))
{
gt_feature_index_delete(features);
features = NULL;
}
gt_node_stream_delete(gff3);
gt_node_stream_delete(cgstream);
gt_node_stream_delete(featstream);
return features;
}
GtNodeVisitor*
agn_gaeval_visitor_new(GtNodeStream *astream, AgnGaevalParams gparams)
{
agn_assert(astream);
// Create the node visitor
GtNodeVisitor *nv = gt_node_visitor_create(gaeval_visitor_class());
AgnGaevalVisitor *v = gaeval_visitor_cast(nv);
v->alignments = gt_feature_index_memory_new();
v->tsvout = NULL;
v->params = gparams;
// Check that sum of weights is 1.0
double weights_total = gparams.alpha + gparams.beta +
gparams.gamma + gparams.epsilon;
if(fabs(weights_total - 1.0) > 0.0001)
{
fprintf(stderr, "[AgnGaevalVisitor::agn_gaeval_visitor_new] warning: "
"sum of weights is not 1.0 %.3lf; integrity calculations will be "
"incorrect\n", weights_total);
}
// Set up node stream to load alignment features into memory
GtQueue *streams = gt_queue_new();
GtNodeStream *stream, *last_stream;
GtHashmap *typestokeep = gt_hashmap_new(GT_HASH_STRING, NULL, NULL);
gt_hashmap_add(typestokeep, "cDNA_match", "cDNA_match");
gt_hashmap_add(typestokeep, "EST_match", "EST_match");
gt_hashmap_add(typestokeep, "nucleotide_match", "nucleotide_match");
stream = agn_filter_stream_new(astream, typestokeep);
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_feature_out_stream_new(last_stream, v->alignments);
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "cDNA_match", "match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "EST_match", "match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
stream = gt_inter_feature_stream_new(last_stream, "nucleotide_match",
"match_gap");
gt_queue_add(streams, stream);
last_stream = stream;
// Process the node stream
GtError *error = gt_error_new();
int result = gt_node_stream_pull(last_stream, error);
if(result == -1)
{
fprintf(stderr, "[AEGeAn::AgnGaevalStream] error parsing alignments: %s\n",
gt_error_get(error));
gt_node_visitor_delete(nv);
return NULL;
}
gt_error_delete(error);
gt_hashmap_delete(typestokeep);
while(gt_queue_size(streams) > 0)
{
stream = gt_queue_get(streams);
gt_node_stream_delete(stream);
}
gt_queue_delete(streams);
return nv;
}
int gt_feature_in_stream_unit_test(GtError *error)
{
GtNodeStream *src, *dest;
GtFeatureIndex *prefeat, *postfeat;
GtRange range1, range1test, range2, range2test;
prefeat = in_stream_test_data(error);
postfeat = gt_feature_index_memory_new();
src = gt_feature_in_stream_new(prefeat);
dest = gt_feature_out_stream_new(src, postfeat);
int result = gt_node_stream_pull(dest, error);
if (result == -1)
return -1;
GtStrArray *seqids = gt_feature_index_get_seqids(postfeat, error);
if (gt_str_array_size(seqids) != 2)
{
gt_error_set(error, "error in feature_in_stream unit test 1: expected 2 "
"seqids, found "GT_WU"", gt_str_array_size(seqids));
return -1;
}
gt_str_array_delete(seqids);
range1test.start = 500; range1test.end = 75000;
range2test.start = 4000; range2test.end = 9500;
gt_feature_index_get_range_for_seqid(postfeat, &range1, "chr1", error);
gt_feature_index_get_range_for_seqid(postfeat, &range2, "scf0001",error);
if (gt_range_compare(&range1, &range1test) ||
gt_range_compare(&range2, &range2test))
{
gt_error_set(error, "error in feature_in_stream unit test 1: incorrect "
"sequence regions");
return -1;
}
gt_feature_index_get_orig_range_for_seqid(postfeat, &range1, "chr1", error);
gt_feature_index_get_orig_range_for_seqid(postfeat, &range2, "scf0001",error);
if (gt_range_compare(&range1, &range1test) ||
gt_range_compare(&range2, &range2test))
{
gt_error_set(error, "error in feature_in_stream unit test 1: incorrect "
"sequence regions");
return -1;
}
gt_feature_index_delete(prefeat);
gt_feature_index_delete(postfeat);
gt_node_stream_delete(src);
gt_node_stream_delete(dest);
prefeat = in_stream_test_data(error);
postfeat = gt_feature_index_memory_new();
src = gt_feature_in_stream_new(prefeat);
dest = gt_feature_out_stream_new(src, postfeat);
gt_feature_in_stream_use_orig_ranges((GtFeatureInStream *)src);
result = gt_node_stream_pull(dest, error);
if (result == -1)
return -1;
range1test.start = 500; range1test.end = 75000;
range2test.start = 4000; range2test.end = 9500;
gt_feature_index_get_range_for_seqid(postfeat, &range1, "chr1", error);
gt_feature_index_get_range_for_seqid(postfeat, &range2, "scf0001",error);
if (gt_range_compare(&range1, &range1test) ||
gt_range_compare(&range2, &range2test))
{
gt_error_set(error, "error in feature_in_stream unit test 1: incorrect "
"sequence regions");
return -1;
}
range1test.start = 1; range1test.end = 100000;
range2test.start = 1; range2test.end = 10000;
gt_feature_index_get_orig_range_for_seqid(postfeat, &range1, "chr1", error);
gt_feature_index_get_orig_range_for_seqid(postfeat, &range2, "scf0001",error);
if (gt_range_compare(&range1, &range1test) ||
gt_range_compare(&range2, &range2test))
{
gt_error_set(error, "error in feature_in_stream unit test 1: incorrect "
"sequence regions");
return -1;
}
gt_feature_index_delete(prefeat);
gt_feature_index_delete(postfeat);
gt_node_stream_delete(src);
gt_node_stream_delete(dest);
return 0;
}
