-
Notifications
You must be signed in to change notification settings - Fork 1
/
genome_tools.txt
105 lines (60 loc) · 3.56 KB
/
genome_tools.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
Genome tools
http://genometools.org/tools/gt.html
http://genometools.org/
https://www.biostars.org/p/111339/
gt gff3 -sort -tidy ref_Amel_4.5_top_level.gff3 | gt stat -genelengthdistri -genescoredistri -exonlengthdistri -exonnumberdistri -intronlengthdistri -cdslengthdistri -o out.txt
gt stat -help
gt gff3 -sort -tidy -sortlines -checkids -fixregionboundaries -force -o test.gff Mp_O_v1.gff
gt gff3 -sort -tidy -sortlines -checkids -fixregionboundaries -retainids yes -force -o Apisum_predictions_PT_20160413.gff3 Apisum_predictions_PT_20160413.gff
gt gff3_to_gtf -force -o GTOOLS.gtf test.gff
# if all else fails!
gffread test2.gff -T -o GTOOLS.gtf
STEPS 1)
convert augustus.gft to gff3
gt gtf_to_gff3 -o test.gff3 -tidy augustus.gtf
STEP 2)
get stats on this new file
gt stat -force -genelengthdistri -genescoredistri -exonlengthdistri -exonnumberdistri -intronlengthdistri -cdslengthdistri -o Mc_braker_stats.txt test.gff3
STEP 1 and 2:)
gt gff3 -sort -tidy Mcerasi_complete_finalv1_pea_aphid_RNASEQ001.gff | gt stat -genelengthdistri -genescoredistri -exonlengthdistri -exonnumberdistri -intronlengthdistri -cdslengthdistri -o out.txt
###############################################################################################
gt gff3 -sort -tidy *.gff | gt stat -force -genelengthdistri -o augustus_genelengthdistri.STAT
wait
gt gff3 -sort -tidy *.gff | gt stat -force -genescoredistri -o augustus_genescoredistri.STAT
wait
gt gff3 -sort -tidy *.gff | gt stat -force -exonlengthdistri -o augustus_exonlengthdistri.STAT
wait
gt gff3 -sort -tidy *.gff | gt stat -force -exonnumberdistri -o augustus_exonnumberdistri.STAT
wait
gt gff3 -sort -tidy *.gff | gt stat -force -intronlengthdistri -o augustus_intronlengthdistri.STAT
wait
gt gff3 -sort -tidy *.gff | gt stat -force -cdslengthdistri -o augustus_cdslengthdistri.STAT
gt gff3 -sort -tidy *.gff3 | gt stat -force -exonlengthdistri -o augustus_exonlengthdistri.STAT
wait
gt gff3 -sort -tidy *.gff3 | gt stat -force -exonnumberdistri -o augustus_exonnumberdistri.STAT
##########################################################################################################
# gff3
gt gff3 -sort -tidy -addintrons *.gff3 | gt stat -force -genelengthdistri -o augustus_genelengthdistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff3 | gt stat -force -genescoredistri -o augustus_genescoredistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff3 | gt stat -force -exonlengthdistri -o augustus_exonlengthdistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff3 | gt stat -force -exonnumberdistri -o augustus_exonnumberdistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff3 | gt stat -force -intronlengthdistri -o augustus_intronlengthdistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff3 | gt stat -force -cdslengthdistri -o augustus_cdslengthdistri.STAT
##########################################################################################################
# gff
gt gff3 -sort -tidy -addintrons *.gff | gt stat -force -genelengthdistri -o augustus_genelengthdistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff | gt stat -force -genescoredistri -o augustus_genescoredistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff | gt stat -force -exonlengthdistri -o augustus_exonlengthdistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff | gt stat -force -exonnumberdistri -o augustus_exonnumberdistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff | gt stat -force -intronlengthdistri -o augustus_intronlengthdistri.STAT
wait
gt gff3 -sort -tidy -addintrons *.gff | gt stat -force -cdslengthdistri -o augustus_cdslengthdistri.STAT