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
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
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+##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