Mercurial > repos > iuc > aegean_locuspocus

diff test-data/parseval_output_test2.txt @ 0:c4ac24510b55 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/aegean commit e6c01517075cab35e620fe1bbdb5fd68e4d1359f"
author iuc
date Sun, 03 Jan 2021 14:58:58 +0000
parents
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/parseval_output_test2.txt	Sun Jan 03 14:58:58 2021 +0000
@@ -0,0 +1,577 @@
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=3631-5899
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01010
+|
+|  prediction genes:
+|    AT1G01010
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01010.1
+     |  prediction transcripts:
+     |    AT1G01010.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR9	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3760	3913	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	3996	4276	.	+	2	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4486	4605	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	4706	5095	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5174	5326	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	CDS	5439	5630	.	+	0	ID=CDS0;Parent=AT1G01010.1
+Chr1	TAIR9	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR9	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	3631	5899	.	+	.	ID=AT1G01010.1;Name=AT1G01010.1;index=1
+Chr1	TAIR10	five_prime_UTR	3631	3759	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3631	3913	.	+	.	Parent=AT1G01010.1
+Chr1	.	start_codon	3760	3762	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3760	3913	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	3914	3995	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	3996	4276	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	3996	4276	.	+	2	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4277	4485	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4486	4605	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4486	4605	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	4606	4705	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	4706	5095	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	4706	5095	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5096	5173	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	exon	5174	5326	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5174	5326	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	.	intron	5327	5438	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	CDS	5439	5630	.	+	0	ID=CDS1;Parent=AT1G01010.1
+Chr1	TAIR10	exon	5439	5899	.	+	.	Parent=AT1G01010.1
+Chr1	.	stop_codon	5628	5630	.	+	.	Parent=AT1G01010.1
+Chr1	TAIR10	three_prime_UTR	5631	5899	.	+	.	Parent=AT1G01010.1
+###
+ |
+     |  CDS structure comparison
+     |    6 reference  CDS segments
+     |    6 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    6 reference  exons
+     |    6 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    2 reference  UTR segments
+     |    2 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=5928-8737
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01020
+|
+|  prediction genes:
+|    AT1G01020
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.1
+     |  prediction transcripts:
+     |    AT1G01020.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR9	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	6915	7069	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7157	7232	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7384	7450	.	-	1	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS2;Parent=AT1G01020.1
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	5928	8737	.	-	.	ID=AT1G01020.1;Name=AT1G01020.1;index=1
+Chr1	TAIR10	three_prime_UTR	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	5928	6263	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	6264	6436	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	three_prime_UTR	6437	6914	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	exon	6437	7069	.	-	.	Parent=AT1G01020.1
+Chr1	.	stop_codon	6915	6917	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	6915	7069	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	.	intron	7070	7156	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7157	7232	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7157	7232	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7233	7383	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7384	7450	.	-	1	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7384	7450	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7451	7563	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7650	7761	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7836	7941	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	7988	8235	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8326	8416	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.1
+Chr1	.	intron	8465	8570	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS4;Parent=AT1G01020.1
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.1
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.1
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.1
+###
+ |
+     |  CDS structure comparison
+     |    9 reference  CDS segments
+     |    9 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    10 reference  exons
+     |    10 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01020.2
+     |  prediction transcripts:
+     |    AT1G01020.2
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR9	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7315	7450	.	-	1	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7564	7649	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7762	7835	.	-	2	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	7942	7987	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8236	8325	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8417	8464	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	CDS	8571	8666	.	-	0	ID=CDS3;Parent=AT1G01020.2
+Chr1	TAIR9	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR9	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	6790	8737	.	-	.	ID=AT1G01020.2;Name=AT1G01020.2;index=1
+Chr1	TAIR10	three_prime_UTR	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	6790	7069	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	three_prime_UTR	7157	7314	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	exon	7157	7450	.	-	.	Parent=AT1G01020.2
+Chr1	.	stop_codon	7315	7317	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7315	7450	.	-	1	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7564	7649	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7564	7649	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7762	7835	.	-	2	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7762	7835	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	7942	7987	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	7942	7987	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8236	8325	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8236	8325	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8417	8464	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8417	8464	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	CDS	8571	8666	.	-	0	ID=CDS5;Parent=AT1G01020.2
+Chr1	TAIR10	exon	8571	8737	.	-	.	Parent=AT1G01020.2
+Chr1	.	start_codon	8664	8666	.	-	.	Parent=AT1G01020.2
+Chr1	TAIR10	five_prime_UTR	8667	8737	.	-	.	Parent=AT1G01020.2
+###
+ |
+     |  CDS structure comparison
+     |    7 reference  CDS segments
+     |    7 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    8 reference  exons
+     |    8 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=11649-13714
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01030
+|
+|  prediction genes:
+|    AT1G01030
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01030.1
+     |  prediction transcripts:
+     |    AT1G01030.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR9	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR9	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	11649	13714	.	-	.	ID=AT1G01030.1;Name=AT1G01030.1;index=1
+Chr1	TAIR10	three_prime_UTR	11649	11863	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	11649	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	stop_codon	11864	11866	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	CDS	11864	12940	.	-	0	Parent=AT1G01030.1
+Chr1	.	start_codon	12938	12940	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	12941	13173	.	-	.	Parent=AT1G01030.1
+Chr1	.	intron	13174	13334	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	five_prime_UTR	13335	13714	.	-	.	Parent=AT1G01030.1
+Chr1	TAIR10	exon	13335	13714	.	-	.	Parent=AT1G01030.1
+###
+ |
+     |  CDS structure comparison
+     |    1 reference  CDS segments
+     |    1 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    2 reference  exons
+     |    2 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    3 reference  UTR segments
+     |    3 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+|-------------------------------------------------
+|---- Locus: seqid=Chr1 range=23146-31227
+|-------------------------------------------------
+|
+|  reference genes:
+|    AT1G01040
+|
+|  prediction genes:
+|    AT1G01040
+|
+|----------
+     |
+     |--------------------------
+     |---- Begin comparison ----
+     |--------------------------
+     |
+     |  reference transcripts:
+     |    AT1G01040.1
+     |  prediction transcripts:
+     |    AT1G01040.1
+     |
+     | reference GFF3:
+##gff-version 3
+Chr1	TAIR9	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR9	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	23519	24451	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24542	24655	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	24752	24962	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25041	25435	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25524	25743	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	25825	25997	.	+	2	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26081	26203	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26292	26452	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26543	26776	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	26862	27012	.	+	1	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27099	27281	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR9	CDS	27372	27533	.	+	0	ID=CDS6;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+     | prediction GFF3:
+##gff-version 3
+Chr1	TAIR10	mRNA	23146	31227	.	+	.	ID=AT1G01040.1;Name=AT1G01040.1;index=1
+Chr1	TAIR10	five_prime_UTR	23146	23518	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	23146	24451	.	+	.	Parent=AT1G01040.1
+Chr1	.	start_codon	23519	23521	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	23519	24451	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24452	24541	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24542	24655	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24542	24655	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24656	24751	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	24752	24962	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	24752	24962	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	24963	25040	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25041	25435	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25041	25435	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25436	25523	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25524	25743	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25524	25743	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25744	25824	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	25825	25997	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	25825	25997	.	+	2	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	25998	26080	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26081	26203	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26081	26203	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26204	26291	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26292	26452	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26292	26452	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26453	26542	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26543	26776	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26543	26776	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	26777	26861	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	26862	27012	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	26862	27012	.	+	1	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27013	27098	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27099	27281	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27099	27281	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	intron	27282	27371	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	exon	27372	27533	.	+	.	Parent=AT1G01040.1
+Chr1	TAIR10	CDS	27372	27533	.	+	0	ID=CDS7;Parent=AT1G01040.1
+Chr1	.	stop_codon	27531	27533	.	+	.	Parent=AT1G01040.1
+###
+ |
+     |  CDS structure comparison
+     |    12 reference  CDS segments
+     |    12 prediction CDS segments
+     |    CDS structures match perfectly!
+     |
+     |  Exon structure comparison
+     |    12 reference  exons
+     |    12 prediction exons
+     |    Exon structures match perfectly!
+     |
+     |  UTR structure comparison
+     |    1 reference  UTR segments
+     |    1 prediction UTR segments
+     |    UTR structures match perfectly!
+     |
+     |    Gene structures match perfectly!
+     |
+     |
+     |--------------------------
+     |----- End comparison -----
+     |--------------------------
+
+============================================================
+========== ParsEval Summary
+============================================================
+
+Started:                31 Dec 2020, 08:38PM
+Reference annotations:  /tmp/tmpuaspc0eb/files/0/4/3/dataset_0436aebb-5e69-4845-b8d6-cc6932c61142.dat
+Prediction annotations: /tmp/tmpuaspc0eb/files/f/a/e/dataset_fae0f82b-28de-405b-9da1-0a227c4b4b92.dat
+Executing command:      parseval -l 0 -t 32 -w -f text -o /tmp/tmpuaspc0eb/files/3/2/7/dataset_327cf1a1-a7ea-412e-ac0f-e23f78ff553a.dat /tmp/tmpuaspc0eb/files/0/4/3/dataset_0436aebb-5e69-4845-b8d6-cc6932c61142.dat /tmp/tmpuaspc0eb/files/f/a/e/dataset_fae0f82b-28de-405b-9da1-0a227c4b4b92.dat 
+
+  Sequences compared
+    Chr1
+
+  Gene loci................................4
+    shared.................................4
+    unique to reference....................0
+    unique to prediction...................0
+
+  Reference annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Prediction annotations
+    genes..................................4
+      average per locus....................1.000
+    transcripts............................5
+      average per locus....................1.250
+      average per gene.....................1.250
+
+  Total comparisons........................5
+    perfect matches........................5 (100.0%)
+      avg. length..........................3607.40 bp
+      avg. # refr exons....................7.60
+      avg. # pred exons....................7.60
+      avg. refr CDS length.................449.40 aa
+      avg. pred CDS length.................449.40 aa
+    perfect matches with mislabeled UTRs...0 (0.0%)
+    CDS structure matches..................0 (0.0%)
+    exon structure matches.................0 (0.0%)
+    UTR structure matches..................0 (0.0%)
+    non-matches............................0 (0.0%)
+
+  CDS structure comparison
+    reference CDS segments.................35
+      match prediction.....................35 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction CDS segments................35
+      match reference......................35 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Exon structure comparison
+    reference exons........................38
+      match prediction.....................38 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction exons.......................38
+      match reference......................38 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  UTR structure comparison
+    reference UTR segments.................12
+      match prediction.....................12 (100.0%)
+      don't match prediction...............0 (0.0%)
+    prediction UTR segments................12
+      match reference......................12 (100.0%)
+      don't match reference................0 (0.0%)
+    Sensitivity............................1.000
+    Specificity............................1.000
+    F1 Score...............................1.000
+    Annotation edit distance...............0.000
+
+  Nucleotide-level comparison      CDS          UTRs         Overall   
+    Matching coefficient:          1.000        1.000        1.000
+    Correlation coefficient:       1.000        1.000        --        
+    Sensitivity:                   1.000        1.000        --        
+    Specificity:                   1.000        1.000        --        
+    F1 Score:                      1.000        1.000        --        
+    Annotation edit distance:      0.000        0.000        --