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comparison test-data/gffcompare_out3.stats @ 5:f99dd58de04f draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/gffcompare commit c8028c2640d2d213da5097df2341a8281fe0b7c8
author iuc
date Fri, 03 Feb 2023 10:57:30 +0000
parents 0f710191a66d
children
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4:0f710191a66d 5:f99dd58de04f
1 # gffcompare v0.11.2 | Command line was: 1 # gffcompare v0.12.6 | Command line was:
2 #gffcompare -r ref_annotation -R -T -e 100 -d 100 -p TCONS gffcompare_in4_gtf 2 #gffcompare -V -r reference_annotation -R --strict-match -e 100 -T -d 100 -p TCONS gffcompare_in4_gtf
3 # 3 #
4 4
5 #= Summary for dataset: gffcompare_in4_gtf 5 #= Summary for dataset: gffcompare_in4_gtf
6 # Query mRNAs : 35 in 29 loci (15 multi-exon transcripts) 6 # Query mRNAs : 35 in 29 loci (15 multi-exon transcripts)
7 # (3 multi-transcript loci, ~1.2 transcripts per locus) 7 # (3 multi-transcript loci, ~1.2 transcripts per locus)
8 # Reference mRNAs : 19 in 6 loci (19 multi-exon) 8 # Reference mRNAs : 35 in 29 loci (15 multi-exon)
9 # Super-loci w/ reference transcripts: 6 9 # Super-loci w/ reference transcripts: 29
10 #-----------------| Sensitivity | Precision | 10 #-----------------| Sensitivity | Precision |
11 Base level: 72.7 | 60.7 | 11 Base level: 100.0 | 100.0 |
12 Exon level: 81.0 | 55.7 | 12 Exon level: 100.0 | 100.0 |
13 Intron level: 81.2 | 64.4 | 13 Intron level: 100.0 | 100.0 |
14 Intron chain level: 10.5 | 13.3 | 14 Intron chain level: 100.0 | 100.0 |
15 Transcript level: 10.5 | 5.7 | 15 Transcript level: 100.0 | 100.0 |
16 Locus level: 33.3 | 6.9 | 16 Locus level: 100.0 | 100.0 |
17 17
18 Matching intron chains: 2 18 Matching intron chains: 15
19 Matching transcripts: 2 19 Matching transcripts: 35
20 Matching loci: 2 20 Matching loci: 29
21 21
22 Missed exons: 2/84 ( 2.4%) 22 Missed exons: 0/122 ( 0.0%)
23 Novel exons: 46/122 ( 37.7%) 23 Novel exons: 0/122 ( 0.0%)
24 Missed introns: 11/69 ( 15.9%) 24 Missed introns: 0/87 ( 0.0%)
25 Novel introns: 28/87 ( 32.2%) 25 Novel introns: 0/87 ( 0.0%)
26 Missed loci: 0/6 ( 0.0%) 26 Missed loci: 0/29 ( 0.0%)
27 Novel loci: 15/29 ( 51.7%) 27 Novel loci: 0/29 ( 0.0%)
28 28
29 Total union super-loci across all input datasets: 21 29 Total union super-loci across all input datasets: 29
30 35 out of 35 consensus transcripts written in gffcmp.annotated.gtf (0 discarded as redundant) 30 35 out of 35 consensus transcripts written in gffcmp.annotated.gtf (0 discarded as redundant)