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view test-data/human_augustus_protein_codingseq_introns_cds_main.gtf @ 1:1fbb1135da16 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 4a8f640dec78899be470ddd1c436fc0d158c80f3
author iuc
date Fri, 10 May 2019 08:52:20 -0400
parents 86c89c3bd99d
children 6519ebe25019
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# 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/000/6/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) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 1 on both strands
# 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
# 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) -----
#
# Constraints/Hints:
# (none)
# Predicted genes for sequence number 2 on both strands
# 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
# ccgcttcctgcttcaagcccgaggcgcccgaggggctgtgcacgtggttgtcgctgagaccgactaccagagtttcgctgtcctgtacctggagcggg
# cggggcagctgtcagtgaagctctacgcccgctcgctccctgtgagcgactcggtcctgagtgggtttgagcagcgggtccaggaggcccacctgact
# gaggaccagatcttctacttccccaagtacggcttctgcgaggctgcagaccagttccacgtcctggacggtgagtgcacagcgggggcaagcatggc
# ggcgtggtga]
# protein sequence = [MLPPGTATLLTLLLAAGSLGQKPQRPRRPASPISTIQPKANFDAQQEQGHRAEATTLHVAPQGTAMAVSTFRKLDGIC
# WQVRQLYGDTGVLGRFLLQARGARGAVHVVVAETDYQSFAVLYLERAGQLSVKLYARSLPVSDSVLSGFEQRVQEAHLTEDQIFYFPKYGFCEAADQF
# HVLDGECTAGASMAAW]
# end gene HS08198.g2
###
# command line:
# 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