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comparison test-data/human_augustus_utr-on.gff @ 0:fcdd4f5c6cfc draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author iuc
date Fri, 20 Oct 2017 03:48:35 -0400
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-1:000000000000 0:fcdd4f5c6cfc
1 ##gff-version 3
2 # This output was generated with AUGUSTUS (version 3.2.3).
3 # AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de),
4 # O. Keller, S. König, L. Gerischer and L. Romoth.
5 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
6 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
7 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
8 # No extrinsic information on sequences given.
9 # Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
10 # human version. Using default transition matrix.
11 # Looks like /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat is in fasta format.
12 # We have hints for 0 sequences and for 0 of the sequences in the input set.
13 #
14 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
15 #
16 # Predicted genes for sequence number 1 on both strands
17 # start gene HS04636.g1
18 HS04636 AUGUSTUS gene 836 8857 1 + . ID=HS04636.g1
19 HS04636 AUGUSTUS transcript 836 8857 . + . ID=HS04636.g1.t1;Parent=HS04636.g1
20 HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=HS04636.g1.t1
21 HS04636 AUGUSTUS exon 836 1017 . + . Parent=HS04636.g1.t1
22 HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=HS04636.g1.t1
23 HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
24 HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
25 HS04636 AUGUSTUS exon 1818 1934 . + . Parent=HS04636.g1.t1
26 HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
27 HS04636 AUGUSTUS exon 2055 2198 . + . Parent=HS04636.g1.t1
28 HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
29 HS04636 AUGUSTUS exon 2852 2995 . + . Parent=HS04636.g1.t1
30 HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
31 HS04636 AUGUSTUS exon 3426 3607 . + . Parent=HS04636.g1.t1
32 HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
33 HS04636 AUGUSTUS exon 4340 4423 . + . Parent=HS04636.g1.t1
34 HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
35 HS04636 AUGUSTUS exon 4543 4789 . + . Parent=HS04636.g1.t1
36 HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
37 HS04636 AUGUSTUS exon 5072 5358 . + . Parent=HS04636.g1.t1
38 HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
39 HS04636 AUGUSTUS exon 5860 6007 . + . Parent=HS04636.g1.t1
40 HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1
41 HS04636 AUGUSTUS exon 6494 8857 . + . Parent=HS04636.g1.t1
42 HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=HS04636.g1.t1
43 # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
44 # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
45 # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
46 # cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
47 # gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
48 # cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
49 # cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
50 # ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
51 # caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
52 # cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
53 # tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
54 # aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
55 # gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
56 # gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
57 # taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
58 # cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
59 # tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
60 # attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
61 # ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
62 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
63 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
64 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
65 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
66 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
67 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
68 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
69 # end gene HS04636.g1
70 ###
71 #
72 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
73 #
74 # Predicted genes for sequence number 2 on both strands
75 # start gene HS08198.g2
76 HS08198 AUGUSTUS gene 86 2105 1 + . ID=HS08198.g2
77 HS08198 AUGUSTUS transcript 86 2105 . + . ID=HS08198.g2.t1;Parent=HS08198.g2
78 HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=HS08198.g2.t1
79 HS08198 AUGUSTUS exon 86 582 . + . Parent=HS08198.g2.t1
80 HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=HS08198.g2.t1
81 HS08198 AUGUSTUS CDS 445 582 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
82 HS08198 AUGUSTUS CDS 812 894 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
83 HS08198 AUGUSTUS exon 812 894 . + . Parent=HS08198.g2.t1
84 HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
85 HS08198 AUGUSTUS exon 1053 1123 . + . Parent=HS08198.g2.t1
86 HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
87 HS08198 AUGUSTUS exon 1208 1315 . + . Parent=HS08198.g2.t1
88 HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
89 HS08198 AUGUSTUS exon 1587 1688 . + . Parent=HS08198.g2.t1
90 HS08198 AUGUSTUS CDS 1772 1848 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1
91 HS08198 AUGUSTUS exon 1772 2105 . + . Parent=HS08198.g2.t1
92 HS08198 AUGUSTUS transcription_end_site 2105 2105 . + . Parent=HS08198.g2.t1
93 # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
94 # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
95 # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
96 # ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
97 # cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
98 # gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
99 # ggcgtggtga]
100 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
101 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
102 # HVLDGECTAGASMAAW]
103 # end gene HS08198.g2
104 ###
105 # command line:
106 # augustus --strand=both --noInFrameStop=false --gff3=on --uniqueGeneId=true --protein=on --codingseq=on --introns=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat --UTR=on --genemodel=complete --species=human