tools/GFF/gtf2gff3.cfg

   1 #This config file allows the user to customize the gtf2gff3
   2 #converter.
   3
   4 [INPUT_FEATURE_MAP]
   5 #Use INPUT_FEATURE_MAP to map your GTF feature types (column 3 in GTF) to valid SO types.
   6 #Don't edit the SO terms below.
   7 #Mapping must be many to one.  That means that exon_this and exon_that could both
   8 #map to the SO term exon, but exon_this could not map to multiple SO terms.
   9
  10 #GTF Term                  #SO Term
  11 gene                      = gene
  12 mRNA                      = mRNA
  13 exon                      = exon
  14 five_prime_utr            = five_prime_UTR
  15 start_codon               = start_codon
  16 CDS                       = CDS
  17 stop_codon                = stop_codon
  18 three_prime_utr           = three_prime_UTR
  19 3UTR                      = three_prime_UTR
  20 3'-UTR                    = three_prime_UTR
  21 5UTR                      = five_prime_UTR
  22 5'-UTR                    = five_prime_UTR
  23 ARS                       = ARS
  24 binding_site              = binding_site
  25 BLASTN_HIT                = nucleotide_match
  26 CDS_motif                 = nucleotide_motif
  27 CDS_parts                 = mRNA_region
  28 centromere                = centromere
  29 chromosome                = chromosome
  30 conflict                  = conflict
  31 Contig                    = contig
  32 insertion                 = insertion
  33 intron                    = intron
  34 LTR                       = long_terminal_repeat
  35 misc_feature              = sequence_feature
  36 misc_RNA                  = transcript
  37 transcript                = transcript
  38 nc_primary_transcript     = nc_primary_transcript
  39 ncRNA                     = ncRNA
  40 nucleotide_match          = nucleotide_match
  41 polyA_signal              = polyA_signal_sequence
  42 polyA_site                = polyA_site
  43 promoter                  = promoter
  44 pseudogene                = pseudogene
  45 real_mRNA                 = mRNA
  46 region                    = region
  47 repeat_family             = repeat_family
  48 repeat_region             = repeat_region
  49 repeat_unit               = repeat region
  50 rep_origin                = origin_of_replication
  51 rRNA                      = rRNA
  52 snoRNA                    = snoRNA
  53 snRNA                     = snRNA
  54 source                    = sequence_feature
  55 telomere                  = telomere
  56 transcript_region         = transcript_region
  57 transposable_element      = transposable_element
  58 transposable_element_gene = transposable_element
  59 tRNA                      = tRNA
  60
  61 [GTF_ATTRB_MAP]
  62 #Maps tags used internally to tags found in your GTF file
  63 #Don't edit the code tags.
  64 #Note that the gene_id and transcript_id tags tell the script
  65 #who the parents of a feature are.
  66
  67 #Code Tag    #GTF Tag
  68 gene_id    = gene_id
  69 gene_name  = gene_name
  70 trnsc_id   = transcript_id
  71 trnsc_name = transcript_name
  72 id         = ID
  73 parent     = Parent
  74 name       = Name
  75
  76 [GFF3_ATTRB_MAP]
  77 #Maps tags used internally to output GFF3 attribute tags.
  78 #Also, when LIMIT_ATTRB is set to 1 only these tags will be
  79 #Output to the GFF3 attributes column.
  80
  81 #Code Tag  #GFF3 Tag
  82 parent   = Parent
  83 id       = ID
  84 name     = Name
  85
  86 [MISC]
  87 # Limit the attribute tags printed to only those in the GFF3_ATTRB_MAP
  88 LIMIT_ATTRB     = 1
  89 #A perl regexp that splits the attributes column into seperate attributes.
  90 ATTRB_DELIMITER = \s*;\s*
  91 #A perl regexp that captures the tag value pairs.
  92 ATTRB_REGEX     = ^\s*(\S+)\s+(\"[^\"]*\")\s*$
  93 #If CDSs are annotated in the GTF file, are the start codons already included (1=yes 0=no)
  94 START_IN_CDS    = 1
  95 #If CDSs are annotated in the GTF file, are the stop codons already included (1=yes 0=no)
  96 STOP_IN_CDS     = 0
  97 #Use the following value (+ or -) for a features strand as the default if an invalid value is passed.
  98 #DEFAULT_STRAND  = +