Mercurial > repos > iuc > funannotate_annotate

comparison test-data/predict_scratch/Genus_species.stats.json @ 5:9feee7fc49a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate commit 2589d2785ca90160a22a5fe14e03311e189ea51d
author iuc
date Thu, 13 Apr 2023 17:13:04 +0000
parents a5baa4ff168d
children
comparison
equal deleted inserted replaced
4:9f2455341fac 5:9feee7fc49a1
1 { 1 {
2 "format": "annotation", 2 "format": "annotation",
3 "command": "/home/abretaud/miniconda3/envs/__funannotate@1.8.7/bin/funannotate predict --input /tmp/tmpm833xrq1/files/e/1/c/dataset_e1c34c74-e579-4cab-b0ed-5ce938ce4e4b.dat --out output --database /home/abretaud/.planemo/planemo_tmp_yntx6ieu/test-data/funannotate_db --species Genus species --isolate --strain --organism other --ploidy 1 --SeqCenter CFMR --SeqAccession 12345 --name FUN_ --numbering 1 --p2g_pident 80 --p2g_prefilter diamond --min_training_models 3 --busco_seed_species fly --busco_db insecta --evm-partition-interval 1500 --min_intronlen 10 --max_intronlen 3000 --min_protlen 50 --repeat_filter overlap blast --cpus 1", 3 "command": "/home/abretaud/miniconda3/envs/__funannotate@1.8.15/bin/funannotate predict --input input/input.fasta --out output --database /home/abretaud/git/iuc_tools/tools/funannotate/test-data/funannotate_db --species Genus species --isolate --strain --organism other --ploidy 1 --SeqCenter CFMR --SeqAccession 12345 --name FUN_ --numbering 1 --p2g_pident 80 --p2g_prefilter diamond --busco_seed_species fly --busco_db insecta --min_training_models 3 --evm-partition-interval 1500 --min_intronlen 10 --max_intronlen 3000 --min_protlen 50 --repeat_filter overlap blast --cpus 1",
4 "organism": "Genus_species", 4 "organism": "Genus_species",
5 "software": { 5 "software": {
6 "name": "funannotate", 6 "name": "funannotate",
7 "version": "1.8.7", 7 "version": "1.8.15",
8 "date": "2021-07-21", 8 "date": "2023-04-13",
9 "resources": { 9 "resources": {
10 "merops": { 10 "merops": {
11 "type": "diamond", 11 "type": "diamond",
12 "version": "12.0", 12 "version": "12.0",
13 "date": "2017-10-04", 13 "date": "2017-10-04",
69 } 69 }
70 } 70 }
71 }, 71 },
72 "assembly": { 72 "assembly": {
73 "num_contigs": 4, 73 "num_contigs": 4,
74 "length": 227430, 74 "length": 732270,
75 "mean_length": 56857.5, 75 "mean_length": 183067.5,
76 "N50": 215740, 76 "N50": 720580,
77 "L50": 1, 77 "L50": 1,
78 "N90": 215740, 78 "N90": 720580,
79 "L90": 1, 79 "L90": 1,
80 "GC_content": 42.86 80 "GC_content": 43.15
81 }, 81 },
82 "annotation": { 82 "annotation": {
83 "genes": 16, 83 "genes": 70,
84 "common_name": 0, 84 "common_name": 0,
85 "mRNA": 16, 85 "mRNA": 69,
86 "tRNA": 0, 86 "tRNA": 1,
87 "ncRNA": 0, 87 "ncRNA": 0,
88 "rRNA": 0, 88 "rRNA": 0,
89 "avg_gene_length": 1660.69, 89 "avg_gene_length": 1544.77,
90 "transcript-level": { 90 "transcript-level": {
91 "CDS_transcripts": 16, 91 "CDS_transcripts": 69,
92 "CDS_five_utr": 0, 92 "CDS_five_utr": 0,
93 "CDS_three_utr": 0, 93 "CDS_three_utr": 0,
94 "CDS_no_utr": 16, 94 "CDS_no_utr": 69,
95 "CDS_five_three_utr": 0, 95 "CDS_five_three_utr": 0,
96 "CDS_complete": 15, 96 "CDS_complete": 68,
97 "CDS_no-start": 0, 97 "CDS_no-start": 0,
98 "CDS_no-stop": 1, 98 "CDS_no-stop": 1,
99 "CDS_no-start_no-stop": 0, 99 "CDS_no-start_no-stop": 0,
100 "total_exons": 42, 100 "total_exons": 209,
101 "total_cds_exons": 42, 101 "total_cds_exons": 209,
102 "multiple_exon_transcript": 13, 102 "multiple_exon_transcript": 58,
103 "single_exon_transcript": 3, 103 "single_exon_transcript": 11,
104 "avg_exon_length": 402.36, 104 "avg_exon_length": 362.67,
105 "avg_protein_length": 359.81, 105 "avg_protein_length": 393.62,
106 "functional": { 106 "functional": {
107 "go_terms": 0, 107 "go_terms": 0,
108 "interproscan": 0, 108 "interproscan": 0,
109 "eggnog": 0, 109 "eggnog": 0,
110 "pfam": 0, 110 "pfam": 0,
111 "cazyme": 0, 111 "cazyme": 0,
112 "merops": 0, 112 "merops": 0,
113 "busco": 0, 113 "busco": 0,
114 "secretion": 0 114 "secretion": 0
115 }, 115 },
116 "pct_exon_overlap_protein_evidence": 11.9 116 "pct_exon_overlap_protein_evidence": 3.81
117 } 117 }
118 } 118 }
119 } 119 }