Mercurial > repos > bgruening > augustus

annotate test-data/human_augustus_protein_codingseq_introns_cds_main.gtf @ 3:f5075dee9d6b draft

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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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f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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1 # This output was generated with AUGUSTUS (version 3.1.0).
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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2 # AUGUSTUS is a gene prediction tool written by Mario Stanke (mario.stanke@uni-greifswald.de),
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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3 # Oliver Keller, Stefanie König and Lizzy Gerischer.
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4 # Please cite: Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler (2008),
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5 # Using native and syntenically mapped cDNA alignments to improve de novo gene finding
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6 # Bioinformatics 24: 637-644, doi 10.1093/bioinformatics/btn013
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7 # No extrinsic information on sequences given.
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f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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8 # Initialising the parameters using config directory /home/bag/projects/code/galaxy/tool_deps/augustus/3.1/iuc/package_augustus_3_1/820bf3789c44/config/ ...
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9 # human version. Using default transition matrix.
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f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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10 # Looks like /tmp/tmpboMLLQ/job_working_directory/000/6/task_0/dataset_9.dat is in fasta format.
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11 # We have hints for 0 sequences and for 0 of the sequences in the input set.
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12 #
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13 # ----- prediction on sequence number 1 (length = 9453, name = HS04636) -----
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14 #
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15 # Constraints/Hints:
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16 # (none)
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17 # Predicted genes for sequence number 1 on both strands
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f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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18 # start gene HS04636.g1
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19 HS04636 AUGUSTUS gene 966 6903 1 + . HS04636.g1
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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20 HS04636 AUGUSTUS transcript 966 6903 . + . HS04636.g1.t1
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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21 HS04636 AUGUSTUS start_codon 966 968 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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22 HS04636 AUGUSTUS intron 1018 1817 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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23 HS04636 AUGUSTUS intron 1935 2054 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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24 HS04636 AUGUSTUS intron 2199 2851 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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25 HS04636 AUGUSTUS intron 2996 3425 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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26 HS04636 AUGUSTUS intron 3608 4339 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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27 HS04636 AUGUSTUS intron 4424 4542 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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28 HS04636 AUGUSTUS intron 4790 5071 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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29 HS04636 AUGUSTUS intron 5359 5859 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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30 HS04636 AUGUSTUS intron 6008 6493 . + . transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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31 HS04636 AUGUSTUS CDS 966 1017 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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32 HS04636 AUGUSTUS CDS 1818 1934 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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33 HS04636 AUGUSTUS CDS 2055 2198 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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34 HS04636 AUGUSTUS CDS 2852 2995 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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35 HS04636 AUGUSTUS CDS 3426 3607 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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36 HS04636 AUGUSTUS CDS 4340 4423 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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37 HS04636 AUGUSTUS CDS 4543 4789 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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38 HS04636 AUGUSTUS CDS 5072 5358 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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39 HS04636 AUGUSTUS CDS 5860 6007 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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40 HS04636 AUGUSTUS CDS 6494 6903 . + 2 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
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41 HS04636 AUGUSTUS stop_codon 6901 6903 . + 0 transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
0
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42 # coding sequence = [atgctcgcccgcgccctgctgctgtgcgcggtcctggcgctcagccatacagcaaatccttgctgttcccacccatgtc
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43 # aaaaccgaggtgtatgtatgagtgtgggatttgaccagtataagtgcgattgtacccggacaggattctatggagaaaactgctcaacaccggaattt
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44 # ttgacaagaataaaattatttctgaaacccactccaaacacagtgcactacatacttacccacttcaagggattttggaacgttgtgaataacattcc
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45 # cttccttcgaaatgcaattatgagttatgtcttgacatccagatcacatttgattgacagtccaccaacttacaatgctgactatggctacaaaagct
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46 # gggaagccttctctaacctctcctattatactagagcccttcctcctgtgcctgatgattgcccgactcccttgggtgtcaaaggtaaaaagcagctt
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47 # cctgattcaaatgagattgtggaaaaattgcttctaagaagaaagttcatccctgatccccagggctcaaacatgatgtttgcattctttgcccagca
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48 # cttcacgcatcagtttttcaagacagatcataagcgagggccagctttcaccaacgggctgggccatggggtggacttaaatcatatttacggtgaaa
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49 # ctctggctagacagcgtaaactgcgccttttcaaggatggaaaaatgaaatatcagataattgatggagagatgtatcctcccacagtcaaagatact
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50 # caggcagagatgatctaccctcctcaagtccctgagcatctacggtttgctgtggggcaggaggtctttggtctggtgcctggtctgatgatgtatgc
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51 # cacaatctggctgcgggaacacaacagagtatgcgatgtgcttaaacaggagcatcctgaatggggtgatgagcagttgttccagacaagcaggctaa
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52 # tactgataggagagactattaagattgtgattgaagattatgtgcaacacttgagtggctatcacttcaaactgaaatttgacccagaactacttttc
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53 # aacaaacaattccagtaccaaaatcgtattgctgctgaatttaacaccctctatcactggcatccccttctgcctgacacctttcaaattcatgacca
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54 # gaaatacaactatcaacagtttatctacaacaactctatattgctggaacatggaattacccagtttgttgaatcattcaccaggcaaattgctggca
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55 # gggttgctggtggtaggaatgttccacccgcagtacagaaagtatcacaggcttccattgaccagagcaggcagatgaaataccagtcttttaatgag
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56 # taccgcaaacgctttatgctgaagccctatgaatcatttgaagaacttacaggagaaaaggaaatgtctgcagagttggaagcactctatggtgacat
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57 # cgatgctgtggagctgtatcctgcccttctggtagaaaagcctcggccagatgccatctttggtgaaaccatggtagaagttggagcaccattctcct
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58 # tgaaaggacttatgggtaatgttatatgttctcctgcctactggaagccaagcacttttggtggagaagtgggttttcaaatcatcaacactgcctca
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59 # attcagtctctcatctgcaataacgtgaagggctgtccctttacttcattcagtgttccagatccagagctcattaaaacagtcaccatcaatgcaag
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60 # ttcttcccgctccggactagatgatatcaatcccacagtactactaaaagaacgttcgactgaactgtag]
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61 # protein sequence = [MLARALLLCAVLALSHTANPCCSHPCQNRGVCMSVGFDQYKCDCTRTGFYGENCSTPEFLTRIKLFLKPTPNTVHYIL
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62 # THFKGFWNVVNNIPFLRNAIMSYVLTSRSHLIDSPPTYNADYGYKSWEAFSNLSYYTRALPPVPDDCPTPLGVKGKKQLPDSNEIVEKLLLRRKFIPD
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63 # PQGSNMMFAFFAQHFTHQFFKTDHKRGPAFTNGLGHGVDLNHIYGETLARQRKLRLFKDGKMKYQIIDGEMYPPTVKDTQAEMIYPPQVPEHLRFAVG
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64 # QEVFGLVPGLMMYATIWLREHNRVCDVLKQEHPEWGDEQLFQTSRLILIGETIKIVIEDYVQHLSGYHFKLKFDPELLFNKQFQYQNRIAAEFNTLYH
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65 # WHPLLPDTFQIHDQKYNYQQFIYNNSILLEHGITQFVESFTRQIAGRVAGGRNVPPAVQKVSQASIDQSRQMKYQSFNEYRKRFMLKPYESFEELTGE
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66 # KEMSAELEALYGDIDAVELYPALLVEKPRPDAIFGETMVEVGAPFSLKGLMGNVICSPAYWKPSTFGGEVGFQIINTASIQSLICNNVKGCPFTSFSV
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67 # PDPELIKTVTINASSSRSGLDDINPTVLLKERSTEL]
3
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68 # end gene HS04636.g1
0
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69 ###
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70 #
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71 # ----- prediction on sequence number 2 (length = 2344, name = HS08198) -----
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72 #
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73 # Constraints/Hints:
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74 # (none)
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75 # Predicted genes for sequence number 2 on both strands
3
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76 # start gene HS08198.g2
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77 HS08198 AUGUSTUS gene 445 1848 1 + . HS08198.g2
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78 HS08198 AUGUSTUS transcript 445 1848 . + . HS08198.g2.t1
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79 HS08198 AUGUSTUS start_codon 445 447 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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80 HS08198 AUGUSTUS intron 583 811 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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81 HS08198 AUGUSTUS intron 895 1052 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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82 HS08198 AUGUSTUS intron 1124 1207 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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83 HS08198 AUGUSTUS intron 1316 1586 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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84 HS08198 AUGUSTUS intron 1689 1771 . + . transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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85 HS08198 AUGUSTUS CDS 445 582 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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86 HS08198 AUGUSTUS CDS 812 894 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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87 HS08198 AUGUSTUS CDS 1053 1123 . + 1 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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88 HS08198 AUGUSTUS CDS 1208 1315 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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89 HS08198 AUGUSTUS CDS 1587 1688 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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90 HS08198 AUGUSTUS CDS 1772 1848 . + 2 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
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91 HS08198 AUGUSTUS stop_codon 1846 1848 . + 0 transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
0
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92 # coding sequence = [atgctgccccctgggactgcgaccctcttgactctgctcctggcagctggctcgctgggccagaagcctcagaggccac
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93 # gccggcccgcatcccccatcagcaccatccagcccaaggccaattttgatgcgcagcaggagcagggccaccgggccgaggccaccacactgcatgtg
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94 # gctccccagggcacagccatggctgtcagtaccttccgaaagctggatgggatctgctggcaggtgcgccagctctatggagacacaggggtcctcgg
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95 # ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
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96 # cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
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97 # gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
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98 # ggcgtggtga]
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99 # protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
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100 # WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
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101 # HVLDGECTAGASMAAW]
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102 # end gene HS08198.g2
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103 ###
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104 # command line:
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f5075dee9d6b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/augustus commit cf04d83d615ff09c4458982282d422fbef7d83ac
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105 # 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