gff3_fix.py-documentation.rst

gff3_fix full documentation

Background

The gff3_fix program fixes 30 error types detected by the program gff3_QC.py. The section 'gff3_fix' lists all error types that currently can be fixed by the gff3_fix.py function (currently 30), including the method used for the fix. (Note that in some cases, this means removing the affected gene model). The section 'Fix function' describes the methods used to fix the error type in question. The section 'Currently no automatic fix available' lists the error types which gff3_fix currently does not handle.

Note that the gff3_fix program requires that all features contain an ID attribute. You can use lib/gff3_ID_generator.py to generate IDs if your gff3 file does not have them for every feature.

gff3_fix

Error code	Error tag	Fix function
Ema0001	Parent feature start and end coordinates exceed those of child features	fix_boundary
Ema0003	This feature is not contained within the parent feature coordinates	fix_boundary
Ema0005	Pseudogene has invalid child feature type	pseudogene
Ema0006	Wrong phase	fix_phase
Ema0007	CDS and parent feature on different strands	delete_model
Ema0009	Incorrectly merged gene parent? Isoforms that do not share coding sequences are found	split
Emr0001	Duplicate transcript found	remove_duplicate_trans
Emr0002	Incorrectly split gene parent?	merge
Esf0001	Feature type may need to be changed to pseudogene	pseudogene
Esf0002	Start/Stop is not a valid 1-based integer coordinate	delete_model
Esf0003	strand information missing	delete_model
Esf0013	White chars not allowed at the start of a line	gff3 parse
Esf0014	##gff-version" missing from the first line	add_gff3_version
Esf0016	##sequence-region seqid may only appear once	remove_directive
Esf0017	Start/End is not a valid integer	delete_model
Esf0018	Start is not less than or equal to end	delete_model
Esf0020	Version is not a valid integer	remove_directive
Esf0021	Unknown directive	remove_directive
Esf0022	Features should contain 9 fields	delete_model
Esf0025	Strand has illegal characters	delete_model
Esf0026	Phase is not 0, 1, or 2, or not a valid integer	fix_phase
Esf0027	Phase is required for all CDS features	fix_phase
Esf0029	Attributes must contain one and only one equal (=) sign	fix_attributes
Esf0030	Empty attribute tag	fix_attributes
Esf0031	Empty attribute value	fix_attributes
Esf0032	Found multiple attribute tags	fix_attributes
Esf0033	Found ", " in a attribute, possible unescaped	fix_attributes
Esf0034	attribute has identical values (count, value)	fix_attributes
Esf0036	Value of a attribute contains unescaped ","	fix_attributes
Esf0041	Unknown reserved (uppercase) attribute	fix_attributes
Esf0041	Unknown reserved (uppercase) attribute	fix_attributes

Fix function

fix function	method
delete_model	remove the whole model from the original gff3 file
remove_duplicate_trans	remove the duplicate transcripts
remove_directive	remove the directive
pseudogene	remove CDS feature and change the feature type of the other feature: first-level → pseudogene; second-level → pseudogenic_transcript; third-level(exon) → pseudogenic_exon
fix_boundary	update the coordinate of the parent by using the minimum and the maximum coordinate of the child feature
fix_phase	correct phase by the function next_phase = (3 - ((CDS['end'] - CDS['start'] + 1 - phase) % 3)) % 3. Note: If the first CDS segment doesn't have a phase, the initial phase will be 0.
fix_attributes	remove empty attribute tag/value; remove the redundant equal sign(=); remove dupliacte attribute; make the first character of the unknown reserved attribute lower case; merge multiple attribute tag and remove the duplicate attribute value; replace , with %2C
split	split the incorrectly merged transcript from a gene model and generate a new gene model
merge	merge the incorrectly split gene model
add_gff3_version	Add ##gff-version 3 to the first line of gff3 file
gff3 parse	parse the gff3 file; ignore blank line in gff3; remove the white chars at the start of a line

Currently no automatic fix available

Error code	Error tag
Ema0002	Protein sequence contains internal stop codons
Ema0004	Incomplete gene feature that should contain at least one mRNA, exon, and CDS
Ema0008	Warning for distinct isoforms that do not share any regions
Emr0003	Duplicate ID
Esf0004	Seqid not found in any ##sequence-region
Esf0005	Start is less than the ##sequence-region start
Esf0006	End is greater than the ##sequence-region end
Esf0007	Seqid not found in the embedded ##FASTA
Esf0008	End is greater than the embedded ##FASTA sequence length
Esf0009	Found Ns in a feature using the embedded ##FASTA
Esf0010	Seqid not found in the external FASTA file
Esf0011	End is greater than the external FASTA sequence length
Esf0012	Found Ns in a feature using the external FASTA
Esf0015	Expecting certain fields in the feature
Esf0019	Version is not "3"
Esf0023	escape certain characters
Esf0024	Score is not a valid floating point number
Esf0035	attribute has unresolved forward reference
Esf0037	Target attribute should have 3 or 4 values
Esf0038	Start/End value of Target attribute is not a valid integer coordinate
Esf0039	Strand value of Target attribute has illegal characters
Esf0040	Value of Is_circular attribute is not "true"