gff3_fix full documentation


The gff3_fix program fixes 30 error types detected by the program The section ‘gff3_fix’ lists all error types that currently can be fixed by the 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/ to generate IDs if your gff3 file does not have them for every feature.


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”