dict2combined_gff_fasta()
dict2gff3()
dict2gff3alignments()
dict2gtf()
gff2dict()
gtf2dict()
is_combined_gff_fasta()
simplifyGO()
split_combined_gff_fasta()
start_end_gap()
validate_and_translate_models()
validate_models()
add_evidence()
auto_score_threshold()
bed2interlap()
best_model_default()
calculate_gene_distance()
calculate_source_order()
check_intron_compatibility()
cluster_by_aed()
cluster_interlap()
cluster_interlap_original()
consensus()
contained()
de_novo_distance()
ensure_unique_names()
extend_utrs()
fasta_length()
filter4evidence()
filter_models_repeats()
generate_consensus()
getAED()
get_loci()
get_overlap()
gff2interlap()
gff_writer()
gffevidence2dict()
map_coords()
order_sources()
parse_data()
reasonable_model()
refine_cluster()
safe_extract_coordinates()
score_aggregator()
score_by_evidence()
score_evidence()
select_best_utrs()
solve_sub_loci()
src_scaling_factor()
sub_cluster()
convert()
gff2cdstranscripts()
gff2combined()
gff2gbff()
gff2gff3()
gff2gtf()
gff2proteins()
gff2tbl()
gff2transcripts()
gtf2cdstranscripts()
gtf2gbff()
gtf2gff()
gtf2proteins()
gtf2tbl()
gtf2transcripts()
tbl2cdstranscripts()
tbl2gbff()
tbl2gff3()
tbl2gtf()
tbl2proteins()
tbl2transcripts()
dict2gbff()
dict2tbl()
drop_alt_coords()
duplicate_coords()
fetch_coords()
findUTRs()
reformatGO()
sbt_writer()
table2asn()
tbl2dict()
FASTA
FASTA.get_seq()
fasta2dict()
fasta2headers()
fasta2lengths()
getSeqRegions()
translate()
annotation_stats()
go_term_dict()
check_file_type()
filter_annotations()
is_gzipped()
is_text_file()
test_table2asn_functional()
zopen()
A module for calculating annotation stats form GFFtk standardized dictionary.
function to output annotation stats from annotation dictionary