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view test-data/human_augustus_utr-on.gtf @ 2:0d425a4b6896 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/augustus commit 0fed5bb024a096dcb5b2858520ba191da7798b6d
author iuc
date Thu, 23 May 2019 18:17:22 -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/000/2/task_0/dataset_1.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	836	8857	1	+	.	HS04636.g1
HS04636	AUGUSTUS	transcript	836	8857	.	+	.	HS04636.g1.t1
HS04636	AUGUSTUS	tss	836	836	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
HS04636	AUGUSTUS	exon	836	1017	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
HS04636	AUGUSTUS	start_codon	966	968	.	+	0	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	exon	1818	1934	.	+	.	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	exon	2055	2198	.	+	.	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	exon	2852	2995	.	+	.	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	exon	3426	3607	.	+	.	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	exon	4340	4423	.	+	.	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	exon	4543	4789	.	+	.	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	exon	5072	5358	.	+	.	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	exon	5860	6007	.	+	.	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	exon	6494	8857	.	+	.	transcript_id "HS04636.g1.t1"; gene_id "HS04636.g1";
HS04636	AUGUSTUS	tts	8857	8857	.	+	.	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	86	2105	1	+	.	HS08198.g2
HS08198	AUGUSTUS	transcript	86	2105	.	+	.	HS08198.g2.t1
HS08198	AUGUSTUS	tss	86	86	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
HS08198	AUGUSTUS	exon	86	582	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
HS08198	AUGUSTUS	start_codon	445	447	.	+	0	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	exon	812	894	.	+	.	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	exon	1053	1123	.	+	.	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	exon	1208	1315	.	+	.	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	exon	1587	1688	.	+	.	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	exon	1772	2105	.	+	.	transcript_id "HS08198.g2.t1"; gene_id "HS08198.g2";
HS08198	AUGUSTUS	tts	2105	2105	.	+	.	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=off --stop=off --stop=off --cds=on --singlestrand=false /tmp/tmpboMLLQ/job_working_directory/000/2/task_0/dataset_1.dat --UTR=on --genemodel=complete --species=human