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Detection of GFF3 format errors

hsiao yi edited this page Jul 24, 2018 · 8 revisions

Start from 1.3.0, please use our readthedocs site for 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_Tag Checked if non-canonical
Ema0001 Parent feature start and end coordinates exceed those of child features Yes
Ema0002 Protein sequence contains internal stop codons No
Ema0003 This feature is not contained within the parent feature coordinates Yes
Ema0004 Incomplete gene feature that should contain at least one mRNA, exon, and CDS No
Ema0005 Pseudogene has invalid child feature type Yes
Ema0006 Wrong phase No
Ema0007 CDS and parent feature on different strands Yes
Ema0008 Warning for distinct isoforms that do not share any regions No
Ema0009 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_Tag Checked if non-canonical
Emr0001 Duplicate transcript found No
Emr0002 Incorrectly split gene parent? No
Emr0003 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_Tag Checked if non-canonical
Esf0001 Feature type may need to be changed to pseudogene Yes
Esf0002 Start/Stop is not a valid 1-based integer coordinate Yes
Esf0003 strand information missing Yes
Esf0004 Seqid not found in any ##sequence-region Yes
Esf0005 Start is less than the ##sequence-region start Yes
Esf0006 End is greater than the ##sequence-region end Yes
Esf0007 Seqid not found in the embedded ##FASTA Yes
Esf0008 End is greater than the embedded ##FASTA sequence length Yes
Esf0009 Found Ns in a feature using the embedded ##FASTA Yes
Esf0010 Seqid not found in the external FASTA file Yes
Esf0011 End is greater than the external FASTA sequence length Yes
Esf0012 Found Ns in a feature using the external FASTA Yes
Esf0013 White chars not allowed at the start of a line Yes
Esf0014 ##gff-version" missing from the first line Yes
Esf0015 Expecting certain fields in the feature Yes
Esf0016 ##sequence-region seqid may only appear once Yes
Esf0017 Start/End is not a valid integer Yes
Esf0018 Start is not less than or equal to end Yes
Esf0019 Version is not "3" Yes
Esf0020 Version is not a valid integer Yes
Esf0021 Unknown directive Yes
Esf0022 Features should contain 9 fields Yes
Esf0023 escape certain characters Yes
Esf0024 Score is not a valid floating point number Yes
Esf0025 Strand has illegal characters Yes
Esf0026 Phase is not 0, 1, or 2, or not a valid integer Yes
Esf0027 Phase is required for all CDS features Yes
Esf0028 Attributes must escape the percent (%) sign and any control characters Yes
Esf0029 Attributes must contain one and only one equal (=) sign Yes
Esf0030 Empty attribute tag Yes
Esf0031 Empty attribute value Yes
Esf0032 Found multiple attribute tags Yes
Esf0033 Found ", " in a attribute, possible unescaped Yes
Esf0034 attribute has identical values (count, value) Yes
Esf0035 attribute has unresolved forward reference Yes
Esf0036 Value of a attribute contains unescaped "," Yes
Esf0037 Target attribute should have 3 or 4 values Yes
Esf0038 Start/End value of Target attribute is not a valid integer coordinate Yes
Esf0039 Strand value of Target attribute has illegal characters Yes
Esf0040 Value of Is_circular attribute is not "true" Yes
Esf0041 Unknown reserved (uppercase) attribute Yes