Mercurial > repos > bgruening > agat

comparison test-data/test09.txt @ 2:e009d8260be2 draft

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 8eb20f601bc1d2a50c8877b7d0ade057e8f86eae
author bgruening
date Thu, 07 Sep 2023 05:29:24 +0000
parents f7c0a0030254
children
comparison
equal deleted inserted replaced
1:6d8444408ff1 2:e009d8260be2
1 --------------------------------------------------------------------------------
2 1
3 Compute transcript with isoforms if any 2 Functional info gene@transcript records:
4 3 _____________________________________________________________________________
5 Number of gene 10 4 | | Nb holded by | Nb gene |
6 Number of transcript 10 5 | | gene | holding it |
7 Number of cds 10 6 |_____________________________________________________________________________|
8 Number of exon 10 7 | name | 10 | 10 |
9 Number of exon in cds 10 8 |_____________________________________________________________________________|
10 Number gene overlapping 4 9 | product | 0 | 0 |
11 Number of single exon gene 10 10 |_____________________________________________________________________________|
12 Number of single exon transcript 10 11 | description | 0 | 0 |
13 mean transcripts per gene 1.0 12 |_____________________________________________________________________________|
14 mean cdss per transcript 1.0 13 | ontology_term | 0 | 0 |
15 mean exons per transcript 1.0 14 |_____________________________________________________________________________|
16 mean exons per cds 1.0 15 | dbxref | 0 | 0 |
17 Total gene length 9795 16 |_____________________________________________________________________________|
18 Total transcript length 9795 17 | dbxref:Genbank | 0 | 0 |
19 Total cds length 9795 18 |_____________________________________________________________________________|
20 Total exon length 9795 19 Nb gene = 10
21 mean gene length 979 20 Nb gene with <name> attribute = 10
22 mean transcript length 979 21 Nb gene without <name> attribute = 0
23 mean cds length 979 22 Nb gene with <product> attribute = 0
24 mean exon length 979 23 Nb gene without <product> attribute = 10
25 mean cds piece length 979 24 Nb gene with <description> attribute = 0
26 % of genome covered by gene 0.9 25 Nb gene without <description> attribute = 10
27 % of genome covered by transcript 0.9 26 Nb gene with <ontology_term> attribute = 0
28 % of genome covered by cds 0.9 27 Nb gene without <ontology_term> attribute = 10
29 % of genome covered by exon 0.9 28 Nb gene with <dbxref> attribute = 0
30 Longest gene 2415 29 Nb gene without <dbxref> attribute = 10
31 Longest transcript 2415 30 Nb gene with <Genbank> dbxref = 0
32 Longest cds 2415 31 Nb gene without <Genbank> dbxref = 10
33 Longest exon 2415 32 _______________________________________________________________________________________________________
34 Longest cds piece 2415 33 | | Nb holded by | Nb transcript | Nb gene with |
35 Shortest gene 399 34 | | transcript | holding it | transcript holding it |
36 Shortest transcript 399 35 |_______________________________________________________________________________________________________|
37 Shortest cds 399 36 | name | 10 | 10 | 10 |
38 Shortest exon 399 37 |_______________________________________________________________________________________________________|
39 Shortest cds piece 399 38 | product | 0 | 0 | 0 |
40 39 |_______________________________________________________________________________________________________|
41 Re-compute transcript without isoforms asked. We remove shortest isoforms if any 40 | description | 0 | 0 | 0 |
42 41 |_______________________________________________________________________________________________________|
43 Number of gene 10 42 | ontology_term | 0 | 0 | 0 |
44 Number of transcript 10 43 |_______________________________________________________________________________________________________|
45 Number of cds 10 44 | dbxref | 0 | 0 | 0 |
46 Number of exon 10 45 |_______________________________________________________________________________________________________|
47 Number of exon in cds 10 46 | dbxref:Genbank | 0 | 0 | 0 |
48 Number gene overlapping 4 47 |_______________________________________________________________________________________________________|
49 Number of single exon gene 10 48 Nb gene = 10
50 Number of single exon transcript 10 49 Nb transcript = 10
51 mean transcripts per gene 1.0 50 Nb gene with <name> attribute = 10
52 mean cdss per transcript 1.0 51 Nb gene without <name> attribute = 0
53 mean exons per transcript 1.0 52 Nb transcript with <name> attribute = 10
54 mean exons per cds 1.0 53 Nb transcript without <name> attribute = 0
55 Total gene length 9795 54 Nb gene with <product> attribute = 0
56 Total transcript length 9795 55 Nb gene without <product> attribute = 10
57 Total cds length 9795 56 Nb transcript with <product> attribute = 0
58 Total exon length 9795 57 Nb transcript without <product> attribute = 10
59 mean gene length 979 58 Nb gene with <description> attribute = 0
60 mean transcript length 979 59 Nb gene without <description> attribute = 10
61 mean cds length 979 60 Nb transcript with <description> attribute = 0
62 mean exon length 979 61 Nb transcript without <description> attribute = 10
63 mean cds piece length 979 62 Nb gene with <ontology_term> attribute = 0
64 % of genome covered by gene 0.9 63 Nb gene without <ontology_term> attribute = 10
65 % of genome covered by transcript 0.9 64 Nb transcript with <ontology_term> attribute = 0
66 % of genome covered by cds 0.9 65 Nb transcript without <ontology_term> attribute = 10
67 % of genome covered by exon 0.9 66 Nb gene with <dbxref> attribute = 0
68 Longest gene 2415 67 Nb gene without <dbxref> attribute = 10
69 Longest transcript 2415 68 Nb transcript with <dbxref> attribute = 0
70 Longest cds 2415 69 Nb transcript without <dbxref> attribute = 10
71 Longest exon 2415 70 Nb gene with Genbank dbxref = 0
72 Longest cds piece 2415 71 Nb gene without Genbank dbxref = 10
73 Shortest gene 399 72 Nb transcript with Genbank dbxref = 0
74 Shortest transcript 399 73 Nb transcript without Genbank dbxref = 10
75 Shortest cds 399 74 _____________________________________________________________________________
76 Shortest exon 399 75 | | Nb holded by | Nb cds |
77 Shortest cds piece 399 76 | | cds | holding it |
78 77 |_____________________________________________________________________________|
79 -------------------------------------------------------------------------------- 78 | name | 10 | 10 |
80 79 |_____________________________________________________________________________|
80 | product | 10 | 10 |
81 |_____________________________________________________________________________|
82 | description | 0 | 0 |
83 |_____________________________________________________________________________|
84 | ontology_term | 12 | 5 |
85 |_____________________________________________________________________________|
86 | dbxref | 10 | 10 |
87 |_____________________________________________________________________________|
88 | dbxref:Genbank | 10 | 10 |
89 |_____________________________________________________________________________|
90 Nb cds = 10
91 Nb cds with <name> attribute = 10
92 Nb cds without <name> attribute = 0
93 Nb cds with <product> attribute = 10
94 Nb cds without <product> attribute = 0
95 Nb cds with <description> attribute = 0
96 Nb cds without <description> attribute = 10
97 Nb cds with <ontology_term> attribute = 5
98 Nb cds without <ontology_term> attribute = 5
99 Nb cds with <dbxref> attribute = 10
100 Nb cds without <dbxref> attribute = 0
101 Nb cds with <Genbank> dbxref = 10
102 Nb cds without <Genbank> dbxref = 0
103 _____________________________________________________________________________
104 | | Nb holded by | Nb exon |
105 | | exon | holding it |
106 |_____________________________________________________________________________|
107 | name | 10 | 10 |
108 |_____________________________________________________________________________|
109 | product | 10 | 10 |
110 |_____________________________________________________________________________|
111 | description | 0 | 0 |
112 |_____________________________________________________________________________|
113 | ontology_term | 12 | 5 |
114 |_____________________________________________________________________________|
115 | dbxref | 10 | 10 |
116 |_____________________________________________________________________________|
117 | dbxref:Genbank | 10 | 10 |
118 |_____________________________________________________________________________|
119 Nb exon = 10
120 Nb exon with <name> attribute = 10
121 Nb exon without <name> attribute = 0
122 Nb exon with <product> attribute = 10
123 Nb exon without <product> attribute = 0
124 Nb exon with <description> attribute = 0
125 Nb exon without <description> attribute = 10
126 Nb exon with <ontology_term> attribute = 5
127 Nb exon without <ontology_term> attribute = 5
128 Nb exon with <dbxref> attribute = 10
129 Nb exon without <dbxref> attribute = 0
130 Nb exon with <Genbank> dbxref = 10
131 Nb exon without <Genbank> dbxref = 0