gff3_QC full documentation

Background

The GFF3 format is flexible and easy to use for most biologists, but this flexibility also allows many errors to be introduced. This QC program aims to detect over 50 types of formatting errors.

Errors are detected by reviewing three types of feature sets in a GFF3 file, and thus are grouped into three categories (Error category – feature type): * Intra-model errors (Ema) – multiple features within a model * Inter-model errors (Emr) – multiple features across models * Single feature errors (Esf) – each single feature.

In addition, we distinguish between errors that apply to protein-coding genes in the ‘canonical’ Sequence ontology style, and errors that apply to ‘non-canonical’ gene models – i.e. non-coding models, or protein-coding genes that are not modeled with gene, mRNA, CDS and exon features. To perform error-checking on a gff3 file that contains non-canonical gene models, you can specify the –noncg argument when running the program.

Below we list all errors currently considered by gff3_QC.py, including the error code, the error tag (a brief explanation of the error), and whether the error is checked for non-canonical gene models (when using the –noncg argument).

View the gff3_QC.py readme for instructions on how to run the program.

Intra-model: Multiple features within a model (Ema)

The error category ‘Intra-model’ collects formatting errors that can be found by jointly considering multiple features within a gene model, such as gene, mRNA, exon, and CDS features. Errors in this category are given an ‘Error_Code’ starting with ‘Ema’.

Error_Code	Error_level	Error_Tag	Checked if non-canonical
Ema0001	Warning	Parent feature start and end coordinates exceed those of child features	Yes
Ema0002	Warning	Protein sequence contains internal stop codons	No
Ema0003	Warning	This feature is not contained within the parent feature coordinates	Yes
Ema0004	Info	Incomplete gene feature that should contain at least one mRNA, exon, and CDS	No
Ema0005	Info	Pseudogene has invalid child feature type	Yes
Ema0006	Info	Wrong phase	No
Ema0007	Warning	CDS and parent feature on different strands	Yes
Ema0008	Warning	Warning for distinct isoforms that do not share any regions	No
Ema0009	Warning	Incorrectly merged gene parent? Isoforms that do not share coding sequences are found	No

Inter-model: Multiple features across models (Emr)

The error category ‘Inter-model’ collects formatting errors that can be found by comparing multiple gene models. Errors in this category are given an ‘Error_Code’ starting with ‘Emr’.

Error_Code	Error_level	Error_Tag	Checked if non-canonical
Emr0001	Warning	Duplicate transcript found	No
Emr0002	Warning	Incorrectly split gene parent?	No
Emr0003	Error	Duplicate ID	Yes

Single feature (Esf)

The error category ‘Single Feature’ collects formatting errors that can be found by searching the GFF3 file line by line. Errors in this category are given an ‘Error_Code’ starting with ‘Esf’.

Error_Code	Error_level	Error_Tag	Checked if non-canonical
Esf0001	Info	Feature type may need to be changed to pseudogene	Yes
Esf0002	Error	Start/Stop is not a valid 1-based integer coordinate	Yes
Esf0003	Error	strand information missing	Yes
Esf0004	Error	Seqid not found in any ##sequence-region	Yes
Esf0005	Error	Start is less than the ##sequence-region start	Yes
Esf0006	Error	End is greater than the ##sequence-region end	Yes
Esf0007	Error	Seqid not found in the embedded ##FASTA	Yes
Esf0008	Error	End is greater than the embedded ##FASTA sequence length	Yes
Esf0009	Info	Found Ns in a feature using the embedded ##FASTA	Yes
Esf0010	Error	Seqid not found in the external FASTA file	Yes
Esf0011	Error	End is greater than the external FASTA sequence length	Yes
Esf0012	Info	Found Ns in a feature using the external FASTA	Yes
Esf0013	Error	White chars not allowed at the start of a line	Yes
Esf0014	Error	##gff-version” missing from the first line	Yes
Esf0015	Error	Expecting certain fields in the feature	Yes
Esf0016	Error	##sequence-region seqid may only appear once	Yes
Esf0017	Error	Start/End is not a valid integer	Yes
Esf0018	Error	Start is not less than or equal to end	Yes
Esf0019	Info	Version is not “3”	Yes
Esf0020	Error	Version is not a valid integer	Yes
Esf0021	Info	Unknown directive	Yes
Esf0022	Error	Features should contain 9 fields	Yes
Esf0023	Error	escape certain characters	Yes
Esf0024	Error	Score is not a valid floating point number	Yes
Esf0025	Error	Strand has illegal characters	Yes
Esf0026	Error	Phase is not 0, 1, or 2, or not a valid integer	Yes
Esf0027	Error	Phase is required for all CDS features	Yes
Esf0028	Info	Attributes must escape the percent (%) sign and any control characters	Yes
Esf0029	Error	Attributes must contain one and only one equal (=) sign	Yes
Esf0030	Error	Empty attribute tag	Yes
Esf0031	Error	Empty attribute value	Yes
Esf0032	Error	Found multiple attribute tags	Yes
Esf0033	Info	Found “, “ in a attribute, possible unescaped	Yes
Esf0034	Info	attribute has identical values (count, value)	Yes
Esf0035	Info	attribute has unresolved forward reference	Yes
Esf0036	Info	Value of a attribute contains unescaped “,”	Yes
Esf0037	Error	Target attribute should have 3 or 4 values	Yes
Esf0038	Error	Start/End value of Target attribute is not a valid integer coordinate	Yes
Esf0039	Error	Strand value of Target attribute has illegal characters	Yes
Esf0040	Error	Value of Is_circular attribute is not “true”	Yes
Esf0041	Error	Unknown reserved (uppercase) attribute	Yes