update information and cases for benchmark

NBISweden · Nov 7, 2019 · 512afe0 · 512afe0
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diff --git a/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/1_test.gff b/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/1_test.gff
@@ -1,3 +1,4 @@
+#GFF1 with attribute "tag value tag value"
 scaffold_5	JGI	exon	442603	443344	.	+	.	gene_id "e_gw1.5.2.1" transcript_id 335995
 scaffold_5	JGI	CDS	442603	443344	.	+	0	gene_id "e_gw1.5.2.1" protein_id 335805 exonNumber 1
 scaffold_5	JGI	start_codon	442603	442605	.	+	0	gene_id "e_gw1.5.2.1"

diff --git a/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/1a_test.gff b/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/1a_test.gff
@@ -1,3 +1,4 @@
+# GFF1 only one value as attribute
 scaffold_5	JGI	exon	442603	443344	.	+	.	geneA
 scaffold_5	JGI	CDS	442603	443344	.	+	0	geneA
 scaffold_5	JGI	start_codon	442603	442605	.	+	0	geneA

diff --git a/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/2_test.gff b/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/2_test.gff
@@ -1,3 +1,4 @@
+# GFF2
 scaffold_5	JGI	exon	442603	443344	.	+	.	gene_id "e_gw1.5.2.1"; transcript_id 335995
 scaffold_5	JGI	CDS	442603	443344	.	+	0	gene_id "e_gw1.5.2.1"; protein_id 335805; exonNumber 1
 scaffold_5	JGI	start_codon	442603	442605	.	+	0	gene_id "e_gw1.5.2.1"

diff --git a/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/2a_test.gff b/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/2a_test.gff
@@ -0,0 +1,9 @@
+#GFF2 as we see often with space before semicolon
+scaffold_5	JGI	exon	442603	443344	.	+	.	gene_id "e_gw1.5.2.1" ; transcript_id 335995
+scaffold_5	JGI	CDS	442603	443344	.	+	0	gene_id "e_gw1.5.2.1" ; protein_id 335805; exonNumber 1
+scaffold_5	JGI	start_codon	442603	442605	.	+	0	gene_id "e_gw1.5.2.1"
+scaffold_5	JGI	exon	443530	443531	.	+	.	gene_id "e_gw1.5.2.1" ; transcript_id 335995
+scaffold_5	JGI	CDS	443530	443531	.	+	2	gene_id "e_gw1.5.2.1" ; protein_id 335805; exonNumber 2
+scaffold_5	JGI	exon	443569	445653	.	+	.	gene_id "e_gw1.5.2.1" ; transcript_id 335995
+scaffold_5	JGI	CDS	443569	445653	.	+	0	gene_id "e_gw1.5.2.1" ; protein_id 335805; exonNumber 3
+scaffold_5	JGI	stop_codon	445651	445653	.	+	0	gene_id "e_gw1.5.2.1"
diff --git a/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/2b_test.gff b/annotation/BILS/Handler/Benchmark/gff_file_type_benchmark/2b_test.gff
@@ -0,0 +1,9 @@
+#GTF2 GFF2.5 as GFF2 but with semicolon at the end
+scaffold_5	JGI	exon	442603	443344	.	+	.	gene_id "e_gw1.5.2.1"; transcript_id 335995;
+scaffold_5	JGI	CDS	442603	443344	.	+	0	gene_id "e_gw1.5.2.1"; protein_id 335805; exonNumber 1;
+scaffold_5	JGI	start_codon	442603	442605	.	+	0	gene_id "e_gw1.5.2.1";
+scaffold_5	JGI	exon	443530	443531	.	+	.	gene_id "e_gw1.5.2.1"; transcript_id 335995;
+scaffold_5	JGI	CDS	443530	443531	.	+	2	gene_id "e_gw1.5.2.1"; protein_id 335805; exonNumber 2;
+scaffold_5	JGI	exon	443569	445653	.	+	.	gene_id "e_gw1.5.2.1"; transcript_id 335995;
+scaffold_5	JGI	CDS	443569	445653	.	+	0	gene_id "e_gw1.5.2.1"; protein_id 335805; exonNumber 3;
+scaffold_5	JGI	stop_codon	445651	445653	.	+	0	gene_id "e_gw1.5.2.1";