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comparison test-data/gffcompare_out2.stats @ 3:84845ad0d35c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8a752199588db982182cbe7fffbcb8512313526
author iuc
date Mon, 27 May 2019 13:53:51 -0400
parents 66f066ca5d60
children 9e282a956012
comparison
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2:66f066ca5d60 3:84845ad0d35c
1 # gffcompare v0.10.6 | Command line was: 1 # gffcompare v0.11.2 | Command line was:
2 #gffcompare -r /tmp/tmp7AvPf0/files/000/dataset_13.dat -R -T -e 100 -d 100 -p TCONS gffcompare_in4_gtf 2 #gffcompare -r ref_annotation -e 100 -d 100 -p TCONS gffcompare_in1_gtf gffcompare_in2_gtf
3 # 3 #
4 4
5 #= Summary for dataset: gffcompare_in4_gtf 5 #= Summary for dataset: gffcompare_in1_gtf
6 # Query mRNAs : 35 in 29 loci (15 multi-exon transcripts) 6 # Query mRNAs : 5 in 5 loci (0 multi-exon transcripts)
7 # (3 multi-transcript loci, ~1.2 transcripts per locus) 7 # (0 multi-transcript loci, ~1.0 transcripts per locus)
8 # Reference mRNAs : 20 in 7 loci (19 multi-exon) 8 # Reference mRNAs : 1 in 1 loci (0 multi-exon)
9 # Super-loci w/ reference transcripts: 6 9 # Super-loci w/ reference transcripts: 1
10 #-----------------| Sensitivity | Precision | 10 #-----------------| Sensitivity | Precision |
11 Base level: 72.6 | 60.7 | 11 Base level: 94.7 | 42.9 |
12 Exon level: 80.0 | 55.7 | 12 Exon level: 100.0 | 40.0 |
13 Intron level: 81.2 | 64.4 | 13 Transcript level: 0.0 | 0.0 |
14 Intron chain level: 10.5 | 13.3 | 14 Locus level: 0.0 | 0.0 |
15 Transcript level: 10.0 | 5.7 |
16 Locus level: 28.6 | 6.9 |
17 15
18 Matching intron chains: 2 16 Matching intron chains: 0
19 Matching transcripts: 2 17 Matching transcripts: 0
20 Matching loci: 2 18 Matching loci: 0
21 19
22 Missed exons: 3/85 ( 3.5%) 20 Missed exons: 0/1 ( 0.0%)
23 Novel exons: 46/122 ( 37.7%) 21 Novel exons: 3/5 ( 60.0%)
24 Missed introns: 11/69 ( 15.9%) 22 Missed loci: 0/1 ( 0.0%)
25 Novel introns: 28/87 ( 32.2%) 23 Novel loci: 3/5 ( 60.0%)
26 Missed loci: 0/7 ( 0.0%)
27 Novel loci: 15/29 ( 51.7%)
28 24
29 Total union super-loci across all input datasets: 21 25 #= Summary for dataset: gffcompare_in2_gtf
30 35 out of 35 consensus transcripts written in gffcmp.annotated.gtf (0 discarded as redundant) 26 # Query mRNAs : 4 in 4 loci (0 multi-exon transcripts)
27 # (0 multi-transcript loci, ~1.0 transcripts per locus)
28 # Reference mRNAs : 1 in 1 loci (0 multi-exon)
29 # Super-loci w/ reference transcripts: 1
30 #-----------------| Sensitivity | Precision |
31 Base level: 31.6 | 18.2 |
32 Exon level: 100.0 | 25.0 |
33 Transcript level: 0.0 | 0.0 |
34 Locus level: 0.0 | 0.0 |
35
36 Matching intron chains: 0
37 Matching transcripts: 0
38 Matching loci: 0
39
40 Missed exons: 0/1 ( 0.0%)
41 Novel exons: 3/4 ( 75.0%)
42 Missed loci: 0/1 ( 0.0%)
43 Novel loci: 3/4 ( 75.0%)
44
45 Total union super-loci across all input datasets: 6
46 (0 multi-transcript, ~1.3 transcripts per locus)
47 8 out of 8 consensus transcripts written in gffcmp.combined.gtf (0 discarded as redundant)