Mercurial > repos > bgruening > augustus_training
diff test-data/human_augustus_utr-on.gff @ 0:86c89c3bd99d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 2896dcfd180800d00ea413a59264ef8b11788b8e
author | bgruening |
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date | Fri, 20 Oct 2017 03:55:35 -0400 |
parents | |
children | 6519ebe25019 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/human_augustus_utr-on.gff Fri Oct 20 03:55:35 2017 -0400 @@ -0,0 +1,106 @@ +##gff-version 3 +# This output was generated with AUGUSTUS (version 3.2.3). +# AUGUSTUS is a gene prediction tool written by M. Stanke (mario.stanke@uni-greifswald.de), +# O. Keller, S. König, L. Gerischer and L. Romoth. +# 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 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 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 +# QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH +# WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE +# KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV +# PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] +# end gene HS04636.g1 +### +# +# ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- +# +# Predicted genes for sequence number 2 on both strands +# 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 +# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF +# HVLDGECTAGASMAAW] +# end gene HS08198.g2 +### +# command line: +# 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