Mercurial > repos > bgruening > augustus
diff test-data/human_augustus_protein_codingseq_introns_cds_main.gtf @ 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_protein_codingseq_introns_cds_main.gtf Wed May 06 14:31:02 2015 -0400 +++ b/test-data/human_augustus_protein_codingseq_introns_cds_main.gtf Fri May 22 04:55:25 2015 -0400 @@ -1,13 +1,13 @@ -# 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 ... +# 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 /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat is in fasta format. +# Looks like /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.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) ----- @@ -15,28 +15,30 @@ # Constraints/Hints: # (none) # Predicted genes for sequence number 1 on both strands -# start gene g1 -HS04636 AUGUSTUS gene 966 6903 1 + . g1 -HS04636 AUGUSTUS transcript 966 6903 . + . g1.t1 -HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "g1.t1"; gene_id "g1"; -HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "g1.t1"; gene_id "g1"; +# start gene HS04636.g1 +HS04636 AUGUSTUS gene 966 6903 1 + . HS04636.g1 +HS04636 AUGUSTUS transcript 966 6903 . + . HS04636.g1.t1 +HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; +HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1"; # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc @@ -63,7 +65,7 @@ # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL] -# end gene g1 +# end gene HS04636.g1 ### # # ----- prediction on sequence number 2 (length = 2344, name = HS08198) ----- @@ -71,20 +73,22 @@ # Constraints/Hints: # (none) # Predicted genes for sequence number 2 on both strands -# start gene g2 -HS08198 AUGUSTUS gene 445 1848 1 + . g2 -HS08198 AUGUSTUS transcript 445 1848 . + . g2.t1 -HS08198 AUGUSTUS intron 583 811 . + . transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "g2.t1"; gene_id "g2"; -HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "g2.t1"; gene_id "g2"; +# start gene HS08198.g2 +HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2 +HS08198 AUGUSTUS transcript 445 1848 . + . HS08198.g2.t1 +HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 583 811 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; +HS08198 AUGUSTUS stop_codon 1846 1848 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2"; # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg @@ -95,7 +99,7 @@ # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF # HVLDGECTAGASMAAW] -# end gene g2 +# end gene HS08198.g2 ### # command line: -# augustus --strand=both --noInFrameStop=false --gff3=off --protein=on --introns=on --start=off --stop=off --cds=on --codingseq=on --singlestrand=false /home/bag/projects/galaxy/galaxy-central/database/files/001/dataset_1149.dat --UTR=off --genemodel=complete --species=human +# augustus --strand=both --noInFrameStop=false --gff3=off --uniqueGeneId=true --protein=on --codingseq=on --introns=on --start=on --stop=on --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat --UTR=off --genemodel=complete --species=human