Mercurial > repos > bgruening > agat

annotate test-data/functional_annot/report.txt @ 6:d6ede73082da draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit df456b8d319fd0a629829fba0f5819117b7936d3
author bgruening
date Fri, 18 Oct 2024 13:34:42 +0000
parents e7449b2c14bf
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
d6ede73082da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit df456b8d319fd0a629829fba0f5819117b7936d3
bgruening
parents: 5
diff changeset
1 10/18/2024
d6ede73082da planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit df456b8d319fd0a629829fba0f5819117b7936d3
bgruening
parents: 5
diff changeset
2 usage: /usr/local/bin/agat_sp_manage_functional_annotation.pl --gff annotation.gff3 --interpro /tmp/tmp710ob4jc/files/9/4/a/dataset_94a00ae6-101b-4441-816d-7fe1c480f05b.dat -pe 5 -o galaxy_functional_annot
3
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
3 --------------------------------------------------------------------------------
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
4
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
5 ------------------------------------- mrna -------------------------------------
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
6 Number of gene 2
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
7 Number of mrna 2
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
8 Number of cds 2
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
9 Number of exon 2
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
10 Number of exon in cds 2
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
11 Number gene overlapping 0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
12 Number of single exon gene 2
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
13 Number of single exon mrna 2
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
14 mean mrnas per gene 1.0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
15 mean cdss per mrna 1.0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
16 mean exons per mrna 1.0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
17 mean exons per cds 1.0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
18 Total gene length (bp) 3294
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
19 Total mrna length (bp) 3294
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
20 Total cds length (bp) 3294
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
21 Total exon length (bp) 3294
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
22 mean gene length (bp) 1647
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
23 mean mrna length (bp) 1647
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
24 mean cds length (bp) 1647
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
25 mean exon length (bp) 1647
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
26 mean cds piece length (bp) 1647
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
27 Longest gene (bp) 2415
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
28 Longest mrna (bp) 2415
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
29 Longest cds (bp) 2415
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
30 Longest exon (bp) 2415
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
31 Longest cds piece (bp) 2415
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
32 Shortest gene (bp) 879
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
33 Shortest mrna (bp) 879
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
34 Shortest cds piece (bp) 879
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
35
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
36 ---------------------------------- transcript ----------------------------------
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
37 Number of gene 8
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
38 Number of transcript 8
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
39 Number of cds 7
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
40 Number of exon 8
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
41 Number of exon in cds 7
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
42 Number gene overlapping 2
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
43 Number of single exon gene 8
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
44 Number of single exon transcript 8
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
45 mean transcripts per gene 1.0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
46 mean cdss per transcript 0.9
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
47 mean exons per transcript 1.0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
48 mean exons per cds 1.0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
49 Total gene length (bp) 6501
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
50 Total transcript length (bp) 6501
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
51 Total cds length (bp) 5688
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
52 Total exon length (bp) 6501
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
53 mean gene length (bp) 812
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
54 mean transcript length (bp) 812
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
55 mean cds length (bp) 812
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
56 mean exon length (bp) 812
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
57 mean cds piece length (bp) 812
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
58 Longest gene (bp) 1149
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
59 Longest transcript (bp) 1149
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
60 Longest cds (bp) 1149
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
61 Longest exon (bp) 1149
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
62 Longest cds piece (bp) 1149
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
63 Shortest gene (bp) 399
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
64 Shortest transcript (bp) 399
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
65 Shortest cds piece (bp) 399
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
66
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
67 _________________________________________________________________________________________________________________________________
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
68 | | Nb Total term | Nb mRNA with term | Nb mRNA updated by term | Nb gene updated by term |
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
69 | | in raw File | in raw File | in our annotation file | in our annotation file |
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
70 |_________________________________________________________________________________________________________________________________|
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
71 | GO | 1 | | 0 | 0 |
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
72 |_________________________________________________________________________________________________________________________________|
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
73 | InterPro | 2 | | 0 | 0 |
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
74 |_________________________________________________________________________________________________________________________________|
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
75 | MetaCyc | 275 | | 0 | 0 |
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
76 |_________________________________________________________________________________________________________________________________|
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
77 | ProSitePatterns | 2 | | 0 | 0 |
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
78 |_________________________________________________________________________________________________________________________________|
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
79 | Reactome | 95 | | 0 | 0 |
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
80 |_________________________________________________________________________________________________________________________________|
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
81
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
82 nb mRNA without Functional annotation (GO,InterPro,MetaCyc,ProSitePatterns,Reactome) = 10
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
83 nb mRNA with Functional annotation (GO,InterPro,MetaCyc,ProSitePatterns,Reactome) = 0
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
84 nb gene without Functional annotation (GO,InterPro,MetaCyc,ProSitePatterns,Reactome) = 10
a6318f87f2cd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/agat commit ac954126686882dd6a64cea30070955344901a00
bgruening
parents:
diff changeset
85 nb gene with Functional annotation (GO,InterPro,MetaCyc,ProSitePatterns,Reactome) = 0