MGKit GFF Specifications

The GFF produced with MGKit follows the conventions of GFF/GTF files but it provides some additional fields in the 9th column which translate to a Python dictionary when an annotation is loaded into an Annotation instance.

The 9th column is a list of key=value item, separated by a semicolon (;); each value is also expected to be quoted with double quotes and the values to not include a semicolon or other characters that can make the parsing difficult. MGKit uses urllib.quote() to encode those characters and also ” ()/”. The mgkit.io.gff.from_gff() uses urllib.unquote() to set the values.

Warning

As the last column translates to a dictionary in the data structures, duplicate keys are not allowed. mgkit.io.gff.from_gff() raises an exception if any are found.

Reserved Values

Any key can be added to a GFF annotation, but MGKit expects a few key to be in the GFF annotation as summarised in the following tables.

Reserved values, used by the scripts

Key	Value	Explanation
seq_id	string	the sequence of the annotation (header in FASTA files)
gene_id	any string	used to identify the gene predicted
db	any string, like UNIPROT-SP, UNIPROT-TR, NCBI-NT	identifies the database used to make the gene_id prediction
taxon_db	any string, like UNIPROT-SP, UNIPROT-TR, NCBI-NT	identifies the database used to make the taxon_id prediction
dbq	integer	identifies the quality of the database, used when filtering annotations
taxon_id	integer	identifies the annotation taxon, NCBI taxonomy is used
uid	string	unique identifier for the annotation, any string is accepted but a value is assigned by using uuid.uuid4()
cov and {any}_cov	integer	coverage for the annotation over all samples, keys ending with _cov indicates coverage for each sample
exp_syn, exp_nonsyn	integer	used for expected number of synonymous and non-synonymous changes for the annotation

The following keys are added by different scripts and may be used in different scripts or annotation methods.

Interpreted Values

Key	Value	Explanation	Used
taxon_name	string	name of the taxon	not used
lineage	string	taxon lineage	not used
EC	comma separated values	list of EC numbers associated to the annotation	used by mgkit.io.gff.Annotation.get_ec()
map_{any}	comma separated values	list of mapping to a specific db (e.g. eggNOG -> map_EGGNOG)	used by mgkit.io.gff.Annotation.get_mapping()
counts_{any}	float	Stores the count data for a sample (e.g. counts_Sample1)	used by script add-gff-info
fpkms_{any}	float	Stores the count data for a sample (e.g. fpkms_Sample1)	used by script add-gff-info
FC	string (no spaces)	each character is a Functional Category in eggNOG (e.g. FJO are 3 different categories)	used by mgkit.io.gff.Annotation.get_fc()