# HG changeset patch
# User charles-bernard
# Date 1476191714 14400
# Node ID e3d439570972f68e14572ddc4b136d58d23d72b2
# Parent  cbb0a78e61e8e3bb2859e689ff9e38fe58d016cc
Uploaded

diff -r cbb0a78e61e8 -r e3d439570972 test-data/alfa_toy-Biofeatures Distribution.pdf
Binary file test-data/alfa_toy-Biofeatures Distribution.pdf has changed
diff -r cbb0a78e61e8 -r e3d439570972 test-data/alfa_toy.bam
Binary file test-data/alfa_toy.bam has changed
diff -r cbb0a78e61e8 -r e3d439570972 test-data/alfa_toy.bedgraph
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alfa_toy.bedgraph	Tue Oct 11 09:15:14 2016 -0400
@@ -0,0 +1,4 @@
+Chr1	149	199	2
+Chr1	299	349	1
+Chr1	499	549	6
+Chr1	1099	1149	1
diff -r cbb0a78e61e8 -r e3d439570972 test-data/alfa_toy.categories_counts
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alfa_toy.categories_counts	Tue Oct 11 09:15:14 2016 -0400
@@ -0,0 +1,5 @@
+#Category,biotype	Counts_in_bam	Size_in_genome
+CDS,protein_coding	300.0	624.0
+five_prime_utr,protein_coding	75.0	250.5
+three_prime_utr,protein_coding	25.0	126.5
+intergenic,intergenic	100.0	249.0
diff -r cbb0a78e61e8 -r e3d439570972 test-data/alfa_toy.gtf
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alfa_toy.gtf	Tue Oct 11 09:15:14 2016 -0400
@@ -0,0 +1,6 @@
+Chr1	ensembl_havana	gene	250	1250	.	+	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1	ensembl_havana	transcript	250	1250	.	+	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1	ensembl_havana	exon	375	1000	.	+	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1	ensembl_havana	CDS	375	1000	.	+	0	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1	ensembl_havana	five_prime_utr	250	375	.	-	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
+Chr1	ensembl_havana	three_prime_utr	1000	1250	.	-	.	gene_id "ENSMUSG00000051951"; gene_biotype "protein_coding";
diff -r cbb0a78e61e8 -r e3d439570972 test-data/alfa_toy.stranded.index
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alfa_toy.stranded.index	Tue Oct 11 09:15:14 2016 -0400
@@ -0,0 +1,11 @@
+#Chr1	1250
+Chr1	249	374	+	protein_coding:gene,transcript
+Chr1	249	374	-	protein_coding:five_prime_utr
+Chr1	374	375	+	protein_coding:exon,CDS
+Chr1	374	375	-	protein_coding:five_prime_utr,three_prime_utr
+Chr1	375	999	+	protein_coding:exon,CDS
+Chr1	375	999	-	antisense
+Chr1	999	1000	+	protein_coding:exon,CDS
+Chr1	999	1000	-	protein_coding:three_prime_utr
+Chr1	1000	1250	+	protein_coding:gene,transcript
+Chr1	1000	1250	-	protein_coding:five_prime_utr,three_prime_utr,exon,CDS
diff -r cbb0a78e61e8 -r e3d439570972 test-data/alfa_toy.unstranded.index
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/alfa_toy.unstranded.index	Tue Oct 11 09:15:14 2016 -0400
@@ -0,0 +1,6 @@
+#Chr1	1250
+Chr1	249	374	.	protein_coding:five_prime_utr,gene,transcript
+Chr1	374	375	.	protein_coding:five_prime_utr,three_prime_utr,exon,CDS
+Chr1	375	999	.	protein_coding:exon,CDS
+Chr1	999	1000	.	protein_coding:three_prime_utr,exon,CDS
+Chr1	1000	1250	.	protein_coding:five_prime_utr,exon,CDS,three_prime_utr,gene,transcript
diff -r cbb0a78e61e8 -r e3d439570972 tool-data/alfa_genomes_indexes.loc.sample
--- a/tool-data/alfa_genomes_indexes.loc.sample	Tue Oct 11 09:14:58 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#<species>	<version>	<release>	<value>	<dbkey>	<name>	<prefix>
-Arabidopsis_thaliana	TAIR10	30	Arabidopsis_t_TAIR10_30	Arabidopsis_t_TAIR10_30	Arabidopsis thaliana: TAIR10	<path_to_alfa_indexes>/Arabidopsis_thaliana.TAIR10.30
-Drosophila_melanogaster	dm6	30	Drosophila_m_dm6_30	Drosophila_m_dm6_30	Drosophila melanogaster: dm6	<path_to_alfa_indexes>/Drosophila_melanogaster.BDGP6.30
-Homo_sapiens	v38	82	Homo_s_v38_82	Homo_s_v38_82	Homo sapiens: v38	<path_to_alfa_indexes>/Homo_sapiens.GRCh38.82
-Mus_musculus	v38	83	Mus_m_v38_83	Mus_m_v38_83	Mus musculus: v38 	<path_to_alfa_indexes>/Mus_musculus.GRCm38.83.chr
\ No newline at end of file
diff -r cbb0a78e61e8 -r e3d439570972 tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Tue Oct 11 09:14:58 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<tables>
-    <!-- Locations of all alfa indexes -->
-    <table name="alfa_indexes" comment_char="#" allow_duplicate_entries="False">
-        <columns>species, version, release, value, dbkey, name, prefix</columns>
-        <file path="tool-data/alfa_genomes_indexes.loc" />
-    </table>
-</tables>
\ No newline at end of file