Mercurial > repos > bgruening > agat
diff test-data/test09.txt @ 2:e009d8260be2 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
| author | bgruening |
|---|---|
| date | Thu, 07 Sep 2023 05:29:24 +0000 |
| parents | f7c0a0030254 |
| children |
line wrap: on
line diff
--- a/test-data/test09.txt Tue May 23 18:05:26 2023 +0000 +++ b/test-data/test09.txt Thu Sep 07 05:29:24 2023 +0000 @@ -1,80 +1,131 @@ --------------------------------------------------------------------------------- -Compute transcript with isoforms if any - -Number of gene 10 -Number of transcript 10 -Number of cds 10 -Number of exon 10 -Number of exon in cds 10 -Number gene overlapping 4 -Number of single exon gene 10 -Number of single exon transcript 10 -mean transcripts per gene 1.0 -mean cdss per transcript 1.0 -mean exons per transcript 1.0 -mean exons per cds 1.0 -Total gene length 9795 -Total transcript length 9795 -Total cds length 9795 -Total exon length 9795 -mean gene length 979 -mean transcript length 979 -mean cds length 979 -mean exon length 979 -mean cds piece length 979 -% of genome covered by gene 0.9 -% of genome covered by transcript 0.9 -% of genome covered by cds 0.9 -% of genome covered by exon 0.9 -Longest gene 2415 -Longest transcript 2415 -Longest cds 2415 -Longest exon 2415 -Longest cds piece 2415 -Shortest gene 399 -Shortest transcript 399 -Shortest cds 399 -Shortest exon 399 -Shortest cds piece 399 - -Re-compute transcript without isoforms asked. We remove shortest isoforms if any - -Number of gene 10 -Number of transcript 10 -Number of cds 10 -Number of exon 10 -Number of exon in cds 10 -Number gene overlapping 4 -Number of single exon gene 10 -Number of single exon transcript 10 -mean transcripts per gene 1.0 -mean cdss per transcript 1.0 -mean exons per transcript 1.0 -mean exons per cds 1.0 -Total gene length 9795 -Total transcript length 9795 -Total cds length 9795 -Total exon length 9795 -mean gene length 979 -mean transcript length 979 -mean cds length 979 -mean exon length 979 -mean cds piece length 979 -% of genome covered by gene 0.9 -% of genome covered by transcript 0.9 -% of genome covered by cds 0.9 -% of genome covered by exon 0.9 -Longest gene 2415 -Longest transcript 2415 -Longest cds 2415 -Longest exon 2415 -Longest cds piece 2415 -Shortest gene 399 -Shortest transcript 399 -Shortest cds 399 -Shortest exon 399 -Shortest cds piece 399 - --------------------------------------------------------------------------------- - +Functional info gene@transcript records: + _____________________________________________________________________________ +| | Nb holded by | Nb gene | +| | gene | holding it | +|_____________________________________________________________________________| +| name | 10 | 10 | +|_____________________________________________________________________________| +| product | 0 | 0 | +|_____________________________________________________________________________| +| description | 0 | 0 | +|_____________________________________________________________________________| +| ontology_term | 0 | 0 | +|_____________________________________________________________________________| +| dbxref | 0 | 0 | +|_____________________________________________________________________________| +| dbxref:Genbank | 0 | 0 | +|_____________________________________________________________________________| +Nb gene = 10 +Nb gene with <name> attribute = 10 +Nb gene without <name> attribute = 0 +Nb gene with <product> attribute = 0 +Nb gene without <product> attribute = 10 +Nb gene with <description> attribute = 0 +Nb gene without <description> attribute = 10 +Nb gene with <ontology_term> attribute = 0 +Nb gene without <ontology_term> attribute = 10 +Nb gene with <dbxref> attribute = 0 +Nb gene without <dbxref> attribute = 10 +Nb gene with <Genbank> dbxref = 0 +Nb gene without <Genbank> dbxref = 10 + _______________________________________________________________________________________________________ +| | Nb holded by | Nb transcript | Nb gene with | +| | transcript | holding it | transcript holding it | +|_______________________________________________________________________________________________________| +| name | 10 | 10 | 10 | +|_______________________________________________________________________________________________________| +| product | 0 | 0 | 0 | +|_______________________________________________________________________________________________________| +| description | 0 | 0 | 0 | +|_______________________________________________________________________________________________________| +| ontology_term | 0 | 0 | 0 | +|_______________________________________________________________________________________________________| +| dbxref | 0 | 0 | 0 | +|_______________________________________________________________________________________________________| +| dbxref:Genbank | 0 | 0 | 0 | +|_______________________________________________________________________________________________________| +Nb gene = 10 +Nb transcript = 10 +Nb gene with <name> attribute = 10 +Nb gene without <name> attribute = 0 +Nb transcript with <name> attribute = 10 +Nb transcript without <name> attribute = 0 +Nb gene with <product> attribute = 0 +Nb gene without <product> attribute = 10 +Nb transcript with <product> attribute = 0 +Nb transcript without <product> attribute = 10 +Nb gene with <description> attribute = 0 +Nb gene without <description> attribute = 10 +Nb transcript with <description> attribute = 0 +Nb transcript without <description> attribute = 10 +Nb gene with <ontology_term> attribute = 0 +Nb gene without <ontology_term> attribute = 10 +Nb transcript with <ontology_term> attribute = 0 +Nb transcript without <ontology_term> attribute = 10 +Nb gene with <dbxref> attribute = 0 +Nb gene without <dbxref> attribute = 10 +Nb transcript with <dbxref> attribute = 0 +Nb transcript without <dbxref> attribute = 10 +Nb gene with Genbank dbxref = 0 +Nb gene without Genbank dbxref = 10 +Nb transcript with Genbank dbxref = 0 +Nb transcript without Genbank dbxref = 10 + _____________________________________________________________________________ +| | Nb holded by | Nb cds | +| | cds | holding it | +|_____________________________________________________________________________| +| name | 10 | 10 | +|_____________________________________________________________________________| +| product | 10 | 10 | +|_____________________________________________________________________________| +| description | 0 | 0 | +|_____________________________________________________________________________| +| ontology_term | 12 | 5 | +|_____________________________________________________________________________| +| dbxref | 10 | 10 | +|_____________________________________________________________________________| +| dbxref:Genbank | 10 | 10 | +|_____________________________________________________________________________| +Nb cds = 10 +Nb cds with <name> attribute = 10 +Nb cds without <name> attribute = 0 +Nb cds with <product> attribute = 10 +Nb cds without <product> attribute = 0 +Nb cds with <description> attribute = 0 +Nb cds without <description> attribute = 10 +Nb cds with <ontology_term> attribute = 5 +Nb cds without <ontology_term> attribute = 5 +Nb cds with <dbxref> attribute = 10 +Nb cds without <dbxref> attribute = 0 +Nb cds with <Genbank> dbxref = 10 +Nb cds without <Genbank> dbxref = 0 + _____________________________________________________________________________ +| | Nb holded by | Nb exon | +| | exon | holding it | +|_____________________________________________________________________________| +| name | 10 | 10 | +|_____________________________________________________________________________| +| product | 10 | 10 | +|_____________________________________________________________________________| +| description | 0 | 0 | +|_____________________________________________________________________________| +| ontology_term | 12 | 5 | +|_____________________________________________________________________________| +| dbxref | 10 | 10 | +|_____________________________________________________________________________| +| dbxref:Genbank | 10 | 10 | +|_____________________________________________________________________________| +Nb exon = 10 +Nb exon with <name> attribute = 10 +Nb exon without <name> attribute = 0 +Nb exon with <product> attribute = 10 +Nb exon without <product> attribute = 0 +Nb exon with <description> attribute = 0 +Nb exon without <description> attribute = 10 +Nb exon with <ontology_term> attribute = 5 +Nb exon without <ontology_term> attribute = 5 +Nb exon with <dbxref> attribute = 10 +Nb exon without <dbxref> attribute = 0 +Nb exon with <Genbank> dbxref = 10 +Nb exon without <Genbank> dbxref = 0