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” |