def map_unmapped_features(unmapped_features, target_chroms, lifted_feature_list, feature_db, feature_hierarchy,
ref_parent_order, args):
if len(unmapped_features) > 0 and target_chroms[0] != args.target:
print("mapping unaligned features to whole genome")
ref_chroms = [args.reference]
target_chroms = [args.target]
return liftover_types.map_unmapped_genes_agaisnt_all(unmapped_features, ref_chroms, target_chroms,
lifted_feature_list, feature_db, feature_hierarchy,
ref_parent_order, args)
return unmapped_features
def main():
#parse args
args = parse_args()
gff = args.g
target_fasta = args.t
reference_fasta = args.r
processes = int(args.p)
output = args.o
chroms_file = args.chroms
db = args.db
infer_transcripts = args.infer_transcripts
infer_genes = args.infer_genes
unplaced_seq = args.unplaced
copies = args.copies
cov_threshold = float(args.a)
seq_threshold = float(args.s)
seq_threshold_copies = float(args.sc)
minimap2_path = args.m
inter_files = args.dir
max_alns = int(args.n)
feature_types_file = args.f
#read chroms
if chroms_file is not None:
ref_chroms, target_chroms = parse_chrm_files(chroms_file)
else:
ref_chroms = [reference_fasta]
target_chroms = [target_fasta]
parent_features_to_lift = get_parent_features_to_lift(feature_types_file)
#lift genes
lifted_feature_list = {}
unmapped_features = []
feature_db, parent_features, intermediate_features, children_features, parent_order = liftover_types.lift_original_annotation(
gff, target_fasta, reference_fasta, ref_chroms, target_chroms,
processes, db, lifted_feature_list, unmapped_features,
infer_transcripts, infer_genes, cov_threshold, seq_threshold,
minimap2_path, inter_files, max_alns, parent_features_to_lift)
unmapped_out = open(args.u, 'w')
if len(unmapped_features) > 0 and target_chroms[0] != target_fasta:
print("mapping unaligned features to whole genome")
ref_chroms = [reference_fasta]
target_chroms = [target_fasta]
unmapped_features = liftover_types.map_unmapped_genes_agaisnt_all(
unmapped_features, target_fasta, reference_fasta, ref_chroms,
target_chroms, processes, lifted_feature_list, feature_db,
parent_features, intermediate_features, children_features,
parent_order, minimap2_path, inter_files, max_alns)
if unplaced_seq is not None and chroms_file is not None:
print("mapping unplaced genes")
ref_chroms, target_chroms = parse_chrm_files(unplaced_seq)
target_chroms = [target_fasta]
liftover_types.map_unplaced_genes(
unmapped_features, target_fasta, reference_fasta, ref_chroms,
target_chroms, processes, lifted_feature_list, feature_db,
parent_features, intermediate_features, children_features,
parent_order, minimap2_path, inter_files, max_alns)
for gene in unmapped_features:
unmapped_out.write(gene.id + "\n")
unmapped_out.close()
if copies:
print("mapping gene copies")
ref_chroms = [reference_fasta]
target_chroms = [target_fasta]
remap = chroms_file is not None
liftover_types.map_extra_copies(
target_fasta, reference_fasta, ref_chroms, target_chroms,
processes, lifted_feature_list, parent_features, children_features,
feature_db, intermediate_features, parent_order,
seq_threshold_copies, minimap2_path, inter_files, remap, max_alns)
write_new_gff.write_new_gff(lifted_feature_list, output, parent_features,
cov_threshold, seq_threshold)