Mercurial > repos > bgruening > augustus
diff test-data/human_augustus_utr-on.gff @ 3:f5075dee9d6b draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
| author | iuc |
|---|---|
| date | Fri, 22 May 2015 04:55:25 -0400 |
| parents | af307d3285c5 |
| children | 4de31938431b |
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--- a/test-data/human_augustus_utr-on.gff Wed May 06 14:31:02 2015 -0400 +++ b/test-data/human_augustus_utr-on.gff Fri May 22 04:55:25 2015 -0400 @@ -1,46 +1,64 @@ ##gff-version 3 -# This output was generated with AUGUSTUS (version 2.7). -# AUGUSTUS is a gene prediction tool for eukaryotes written by Mario Stanke (mario.stanke@uni-greifswald.de) -# and Oliver Keller (keller@cs.uni-goettingen.de). +# This output was generated with AUGUSTUS (version 3.1.0). +# AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de), +# Oliver Keller, Stefanie König and Lizzy Gerischer. # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008), # Using native and syntenically mapped cDNA alignments to improve de novo gene finding # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013 # No extrinsic information on sequences given. -# Initialising the parameters ... -# human version. Using species specific transition matrix: /home/bag/Downloads/augustus.2.7/config/species/human/human_trans_shadow_partial_utr.pbl -# Looks like ./examples/example.fa is in fasta format. +# Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ... +# human version. Using default transition matrix. +# Looks like /tmp/tmpboMLLQ/job_working_directory/000/4/task_0/dataset_5.dat is in fasta format. # We have hints for 0 sequences and for 0 of the sequences in the input set. # # ----- prediction on sequence number 1 (length = 9453, name = HS04636) ----- # # Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 836 8857 1 + . ID=g1 -HS04636 AUGUSTUS transcript 836 8857 . + . ID=g1.t1;Parent=g1 -HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=g1.t1 -HS04636 AUGUSTUS exon 836 1017 . + . Parent=g1.t1 -HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=g1.t1 -HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 1818 1934 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 2055 2198 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 2852 2995 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 3426 3607 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 4340 4423 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 4543 4789 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 5072 5358 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 5860 6007 . + . Parent=g1.t1 -HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=g1.t1.cds;Parent=g1.t1 -HS04636 AUGUSTUS exon 6494 8857 . + . Parent=g1.t1 -HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 Parent=g1.t1 -HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=g1.t1 +# start gene HS04636.g1 +HS04636 AUGUSTUS gene 836 8857 1 + . ID=HS04636.g1 +HS04636 AUGUSTUS transcript 836 8857 . + . ID=HS04636.g1.t1;Parent=HS04636.g1 +HS04636 AUGUSTUS transcription_start_site 836 836 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 836 1017 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS start_codon 966 968 . + 0 Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 966 1017 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 1818 1934 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 1818 1934 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 2055 2198 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 2055 2198 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 2852 2995 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 2852 2995 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 3426 3607 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 3426 3607 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 4340 4423 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 4340 4423 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 4543 4789 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 4543 4789 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 5072 5358 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 5072 5358 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 5860 6007 . + 0 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 5860 6007 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS CDS 6494 6903 . + 2 ID=HS04636.g1.t1.cds;Parent=HS04636.g1.t1 +HS04636 AUGUSTUS exon 6494 8857 . + . Parent=HS04636.g1.t1 +HS04636 AUGUSTUS transcription_end_site 8857 8857 . + . Parent=HS04636.g1.t1 +# coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc +# aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt +# ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc +# cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct +# gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt +# cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca +# cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa +# ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact +# caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc +# cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa +# tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc +# aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca +# gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca +# gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag +# taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat +# cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct +# tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca +# attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag +# ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag] # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG @@ -48,30 +66,41 @@ # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] -# end gene g1 +# end gene HS04636.g1 ### # # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- # # Predicted genes for sequence number 2 on both strands -# start gene g2 -HS08198 AUGUSTUS gene 86 2344 1 + . ID=g2 -HS08198 AUGUSTUS transcript 86 2344 . + . ID=g2.t1;Parent=g2 -HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=g2.t1 -HS08198 AUGUSTUS exon 86 582 . + . Parent=g2.t1 -HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=g2.t1 -HS08198 AUGUSTUS CDS 445 582 . + 0 ID=g2.t1.cds;Parent=g2.t1 -HS08198 AUGUSTUS CDS 812 894 . + 0 ID=g2.t1.cds;Parent=g2.t1 -HS08198 AUGUSTUS exon 812 894 . + . Parent=g2.t1 -HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=g2.t1.cds;Parent=g2.t1 -HS08198 AUGUSTUS exon 1053 1123 . + . Parent=g2.t1 -HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=g2.t1.cds;Parent=g2.t1 -HS08198 AUGUSTUS exon 1208 1315 . + . Parent=g2.t1 -HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=g2.t1.cds;Parent=g2.t1 -HS08198 AUGUSTUS exon 1587 1688 . + . Parent=g2.t1 +# start gene HS08198.g2 +HS08198 AUGUSTUS gene 86 2105 1 + . ID=HS08198.g2 +HS08198 AUGUSTUS transcript 86 2105 . + . ID=HS08198.g2.t1;Parent=HS08198.g2 +HS08198 AUGUSTUS transcription_start_site 86 86 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 86 582 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS start_codon 445 447 . + 0 Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 445 582 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 812 894 . + 0 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 812 894 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 1053 1123 . + 1 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 1053 1123 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 1208 1315 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 1208 1315 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 1587 1688 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 1587 1688 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS CDS 1772 1848 . + 2 ID=HS08198.g2.t1.cds;Parent=HS08198.g2.t1 +HS08198 AUGUSTUS exon 1772 2105 . + . Parent=HS08198.g2.t1 +HS08198 AUGUSTUS transcription_end_site 2105 2105 . + . Parent=HS08198.g2.t1 +# coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac +# gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg +# gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg +# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg +# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact +# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc +# ggcgtggtga] # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC -# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKY] -# end gene g2 +# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF +# HVLDGECTAGASMAAW] +# end gene HS08198.g2 ### # command line: -# ./bin/augustus --species=human --UTR=on --gff3=on ./examples/example.fa +# 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