GFF3 Feature Tally
Tally GFF3 feature types while respecting comments and the embedded FASTA boundary.
Description
GFF3 stores genomic feature types with coordinates, strand and phase.
GFF3 stores genomic feature types with coordinates, strand and phase. An embedded FASTA boundary separates feature records from sequence content.1
Tally GFF3 feature types while respecting comments and the embedded FASTA boundary.
When to use GFF3 Feature Tally
Use this for the following task: Tally GFF3 feature types while respecting comments and the embedded FASTA boundary.
Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
How to use GFF3 Feature Tally and understand its results
- Prepare the caller-filtered sequences, counts, coordinates or annotations requested below. Keep identifiers and paired lists aligned on the same reference.
- Enter gff3 using the field table, then run the tool.
- Read featureTypes, featureCounts, recordCount. Interpret flags, units, ordering and placeholder values using the rules below.
- Review any reported issue or failed check, correct the supplied values when appropriate, and verify the result in its intended context.
| Input field | Meaning | Value type and bounds | Requirement |
|---|---|---|---|
| gff3 | GFF3 feature records or a document. Counts records, including repeated IDs; stops at ##FASTA. Does not validate ontology or parent relationships. | string; maximum text length 1000000 | Required |
Skip blank and leading-# lines, stopping at exact ##FASTA. Require nine tab-separated fields, safe positive 1-based inclusive coordinates, valid strand/phase and a finite score or dot. CDS needs phase 0–2. Sort type tallies lexically.2
recordCount = sum of type tallies before ##FASTA This summarizes the declared operation. Units, indexing, inclusivity and exceptional cases are explained in the surrounding text.
| Output field | Meaning | Value type |
|---|---|---|
| featureTypes | Feature types | list of string |
| featureCounts | Feature counts | list of integer |
| recordCount | Record count | integer |
{
"input": {
"gff3": "##gff-version 3\nchr1\tx\tgene\t1\t10\t.\t+\t.\tID=g1\nchr1\tx\texon\t1\t5\t.\t+\t.\tParent=g1\n"
},
"output": {
"featureTypes": [
"exon",
"gene"
],
"featureCounts": [
1,
1
],
"recordCount": 2
}
}Limitations and assumptions
This is a feature-field audit and tally, not validation of all attributes, parent relations or complete gene models.
The tool operates on supplied local data; alignment, filtering and annotation must already be appropriate for the stated calculation. Malformed requests produce input errors. A successfully evaluated request can still contain false flags, empty result lists or a result outside the supplied threshold; those outcomes have the meanings stated above.
Alternative or Complementary methods
Choose FASTA Line Width Audit for this operation: Audit wrapping of nucleotide or protein FASTA records at a caller-supplied width, allowing a shorter final sequence line. For a complementary task, use Gene Model Junction Support for this operation: Validate exon-model introns against coordinate-matched observed junction read evidence.
Further background: Background specification: GFF3 Feature Tally.
References
-
Background specification: GFF3 Feature Tally — github.com
-
GFF3 Feature Tally — tool.io
Similar or alternative tools
- FASTA Line Width Audit
Audit wrapping of nucleotide or protein FASTA records at a caller-supplied width, allowing a shorter final sequence line.
- Gene Model Junction Support
Validate exon-model introns against coordinate-matched observed junction read evidence.