convert_gff_to_ncbi_tbl.py about biocode HOT 3 CLOSED

Stan - Our code assumes input GFF3 following both the physical format and gene graph modeling described in the GFF3 specification.

The important part here is that CDS/exon features should have a type of RNA as their parent, where you have them attached to a gene feature. In that specification page search for this string "Here is how this gene should be described using GFF3".

The one thing not shown in that representation is where to attach annotation. We attach annotation features to the polypeptide for coding genes and the RNA feature for non-coding. Example:

gi|169887498|gb|CP000948.1|     .       gene    3734    5020    .       +       .       ID=1_4
gi|169887498|gb|CP000948.1|     .       mRNA    3734    5020    .       +       .       ID=1_4_mRNA;Parent=1_4
gi|169887498|gb|CP000948.1|     .       CDS     3734    5020    .       +       0       ID=1_4_cds;Parent=1_4_mRNA
gi|169887498|gb|CP000948.1|     .       exon    3734    5020    .       +       .       ID=1_4_exon;Parent=1_4_mRNA
gi|169887498|gb|CP000948.1|     .       polypeptide     3734    5020    .       +       .       ID=1_4_polypeptide;Parent=1_4_mRNA;product_name=threonine synthase;Dbxref=EC:4.2.3.1;Ontology_term=GO:0004795,GO:0009088

from biocode.

from biocode.

You should also note that there are many GFF3-related utility scripts within biocode's 'gff' directory which could help here. Some scripts convert common tool 'gff' output to actual gff3 while others can be used to manipulate conventions within a gff file more directly. Hopefully this helps.

from biocode.