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Weird distance and internals bug #13

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jenzopr opened this issue Jun 19, 2017 · 3 comments
Open

Weird distance and internals bug #13

jenzopr opened this issue Jun 19, 2017 · 3 comments

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@jenzopr
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jenzopr commented Jun 19, 2017

When uropa is run with the config.json:

"queries":[
		  {"feature":"gene", "distance":17, "internals":"T", "show.attributes":["gene_id", "gene_name", "gene_type"]}
          ],
"priority": "F",
"gtf": "x.gtf",
"bed": "x.bed"
}

and x.bed:

chr1	5	7	Other
chr1	8	55	L1

and x.gtf:

chr1	HAVANA	gene	1	10	.	+	.	gene_id "ENSMUSG00000102693"; gene_type "TEC"; gene_status "KNOWN"; gene_name "4933401J01Rik"; level 2; havana_gene "OTTMUSG00000049935.1";
chr1	ENSEMBL	gene	50	100	.	+	.	gene_id "ENSMUSG00000064842"; gene_type "snRNA"; gene_status "KNOWN"; gene_name "Gm26206"; level 3;
chr1	HAVANA	gene	200	300	.	-	.	gene_id "ENSMUSG00000051951"; gene_type "protein_coding"; gene_status "KNOWN"; gene_name "Xkr4"; level 2; havana_gene "OTTMUSG00000026353.2";

the second peak (8 - start, 32 - center, 55 - end) is not annotated to the second gene (50 - start, 100 - end).
When the distance is allowed to be 18, the peak is annotated. It seems that in the case of overlapStart, the internals rescue does not work as intended.

@ckuenne
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ckuenne commented Jun 20, 2017

i adapted the docu to the intended changes to the internals parameter: UROPA/docs_rst/config.rst

@jenzopr
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jenzopr commented Jun 20, 2017

The default should be internals = 'none' to match the previous behavior.

@jenzopr
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jenzopr commented Jun 20, 2017

@afust allowed values are
"center", "any", "none"

For backwards compatibility, also
"T", "True", "Y", "Yes" are allowed and will be treated as "center",
"F", "False", "N", "No" are allowed and will be treated as "none".

@jenzopr jenzopr added this to the Version 2 milestone Jun 26, 2017
@jenzopr jenzopr added this to Work packages in UROPA Sprint: Version 2 Oct 26, 2017
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