#This config file allows the user to customize the gtf2gff3 #converter. [INPUT_FEATURE_MAP] #Use INPUT_FEATURE_MAP to map your GTF feature types (column 3 in GTF) to valid SO types. #Don't edit the SO terms below. #Mapping must be many to one. That means that exon_this and exon_that could both #map to the SO term exon, but exon_this could not map to multiple SO terms. #GTF Term #SO Term gene = gene mRNA = mRNA exon = exon five_prime_utr = five_prime_UTR start_codon = start_codon CDS = CDS stop_codon = stop_codon three_prime_utr = three_prime_UTR 3UTR = three_prime_UTR 3'-UTR = three_prime_UTR 5UTR = five_prime_UTR 5'-UTR = five_prime_UTR ARS = ARS binding_site = binding_site BLASTN_HIT = nucleotide_match CDS_motif = nucleotide_motif CDS_parts = mRNA_region centromere = centromere chromosome = chromosome conflict = conflict Contig = contig insertion = insertion intron = intron LTR = long_terminal_repeat misc_feature = sequence_feature misc_RNA = transcript transcript = transcript nc_primary_transcript = nc_primary_transcript ncRNA = ncRNA nucleotide_match = nucleotide_match polyA_signal = polyA_signal_sequence polyA_site = polyA_site promoter = promoter pseudogene = pseudogene real_mRNA = mRNA region = region repeat_family = repeat_family repeat_region = repeat_region repeat_unit = repeat region rep_origin = origin_of_replication rRNA = rRNA snoRNA = snoRNA snRNA = snRNA source = sequence_feature telomere = telomere transcript_region = transcript_region transposable_element = transposable_element transposable_element_gene = transposable_element tRNA = tRNA [GTF_ATTRB_MAP] #Maps tags used internally to tags found in your GTF file #Don't edit the code tags. #Note that the gene_id and transcript_id tags tell the script #who the parents of a feature are. #Code Tag #GTF Tag gene_id = gene_id gene_name = gene_name trnsc_id = transcript_id trnsc_name = transcript_name id = ID parent = Parent name = Name [GFF3_ATTRB_MAP] #Maps tags used internally to output GFF3 attribute tags. #Also, when LIMIT_ATTRB is set to 1 only these tags will be #Output to the GFF3 attributes column. #Code Tag #GFF3 Tag parent = Parent id = ID name = Name [MISC] # Limit the attribute tags printed to only those in the GFF3_ATTRB_MAP LIMIT_ATTRB = 1 #A perl regexp that splits the attributes column into seperate attributes. ATTRB_DELIMITER = \s*;\s* #A perl regexp that captures the tag value pairs. ATTRB_REGEX = ^\s*(\S+)\s+(\"[^\"]*\")\s*$ #If CDSs are annotated in the GTF file, are the start codons already included (1=yes 0=no) START_IN_CDS = 1 #If CDSs are annotated in the GTF file, are the stop codons already included (1=yes 0=no) STOP_IN_CDS = 0 #Use the following value (+ or -) for a features strand as the default if an invalid value is passed. #DEFAULT_STRAND = +