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Update README.md
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Juke34 authored Feb 23, 2024
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Expand Up @@ -352,14 +352,14 @@ $omniscient{other}{level}{level2}{featureTypeZ} = value featureTypeZ
#### How does the AGAT parser work
[<img align="right" src="docs/img/agat_parsing_overview.jpg" width="400" height="250" />](https://nbis.se)
[<img align="right" src="docs/img/agat_parsing_overview.jpg" width="500" height="250" />](https://nbis.se)
The AGAT parser phylosophy:
* 1) Parse by Parent/child relationship or gene_id/transcript_id relationship.
* 2) ELSE Parse by a common tag (an attribute value shared by feature that must be grouped together. By default we are using locus_tag but can be set by parameter).
* 3) ELSE Parse sequentially (mean group features in a bucket, and the bucket change at each level2 feature, and bucket are join in a common tag at each new L1 feature).
**/!\\** Case with only level3 features (i.e rast or some prokka files, sequential will not work as expected. Indeed all features will be the child of only one newly created Parent. To create a parent per feature or group of features, a common tag must be used to group them correctly. We use `gene_id` and `locus_tag` by default but you can set up the one of your choice)
**/!\\** Cases with only level3 features (i.e rast or some prokka files), **sequential parsing** may not work as expected if Parent/ID gene_id/transcript_id attributes are missing. Indeed all features will be the child of only one newly created Parent. To create a parent per feature or group of features, a common tag must be used to group them correctly (by default `gene_id` and `locus_tag` but you can set up the ones of your choice)
To resume by priority of way to parse: **Parent/child relationship > locus_tag > sequential.**
The parser may used only one or a mix of these approaches according of the peculiarity of the gtf/gff file you provide.
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