Translate gene annotation (intervals) from a bed format to the node id space of a variation graph. The bed format is only allowed to have of four columns (see below).
If you want to convert gff to bed file, use the gff2bed.py script
gfa_annotate 0.1.0
Sebastian V
Overlap annotation and genome graphs
USAGE:
gfa_annotate -g <gfa> -b <bed> -o <output>
FLAGS:
-h, --help Print help information
-V, --version Print version information
Input:
-b <bed> bed file
-g <gfa> input gfa
Additional features:
-f, --fraction Report fraction of how much is covered
-l, --length Report length in the table
Output:
-o <output> Output file
- Tab-separated
- Only four columns
Example:
| TAIR10 | 100 | 200 | gene |
|---|---|---|---|
| OR |
| TAIR10 | 250 | 350 | AT1234 |
|---|
| Col | Type | Description |
|---|---|---|
| 1 | int | Node id |
| 2* | String list | Type |
| 3 | int | Length (opt) |
*If the fraction parameter is set, the fraction value in added after the entry. If the same entry has two different fractions, entry is represented twice with different fractions. Must be here because it is specific to the annotation and not the node.
Default
| Node id | Feature |
|---|---|
| 11 | AT1234 |
| 12 | AT14213, AT4321 |
With fraction and length:
| node id | Feature;Fraction,[] | Length |
|---|---|---|
| 11 | AT1234;1 | 21 |
| 12 | AT14213;0.75,AT4321;1 | 4 |
Requirements:
- python3
- argparse
- logging
usage: gff2bed.py [-h] -g GFF [-a ATTRIBUTE] -o OUTPUT
optional arguments:
-h, --help show this help message and exit
-g GFF, --gff GFF Gff file
-a ATTRIBUTE, --attribute ATTRIBUTE
Extract this attribute (except of type)
-o OUTPUT, --output OUTPUT
Output file
If you want the inverse: "Which feature/attribute is covered by which node?", you can use this python script.
usage: attribute2node.py [-h] -i INPUT -o OUTPUT
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
gfa_annotate output file
-o OUTPUT, --output OUTPUT
Output file
Adding intergenic information to the node -> feature data:
Check out ./data/exmaple_data/
cargo test
How many nodes are not fully covered?
Annotation from one accession:
Annotation from all accessions:
- Feature --> Node list (inverse of the output right now)
- Report stuff which is not covered by anything (like report all nodes no matter what)
- Update plots + the pipeline the plots were created.
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