Mercurial > repos > charles-bernard > alfa

changeset 40:d88413b718de draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author charles-bernard
date Thu, 21 Dec 2017 09:57:09 -0500
parents 5adde3d05247
children 1e508bfd35c5
files alfa/alfa/alfa/test-data/alfa_toy-Biofeatures Distribution.pdf alfa/alfa/alfa/test-data/alfa_toy.bam alfa/alfa/alfa/test-data/alfa_toy.bedgraph alfa/alfa/alfa/test-data/alfa_toy.categories_counts alfa/alfa/alfa/test-data/alfa_toy.gtf alfa/alfa/alfa/test-data/alfa_toy.stranded.index alfa/alfa/alfa/test-data/alfa_toy.unstranded.index alfa/alfa/alfa/tool-data/alfa_indexes.loc.sample alfa/test-data/alfa_toy.bam alfa/test-data/alfa_toy.bedgraph alfa/test-data/alfa_toy.categories_counts alfa/test-data/alfa_toy.gtf alfa/test-data/alfa_toy.stranded.index alfa/test-data/alfa_toy.unstranded.index alfa/tool-data/alfa_indexes.loc.sample
diffstat 15 files changed, 0 insertions(+), 68 deletions(-) [+]
line wrap: on
line diff
Binary file alfa/alfa/alfa/test-data/alfa_toy-Biofeatures Distribution.pdf has changed
Binary file alfa/alfa/alfa/test-data/alfa_toy.bam has changed
--- a/alfa/alfa/alfa/test-data/alfa_toy.bedgraph	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Chr1	149	199	2
-Chr1	299	349	1
-Chr1	499	549	6
-Chr1	1099	1149	1
--- a/alfa/alfa/alfa/test-data/alfa_toy.categories_counts	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#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
--- a/alfa/alfa/alfa/test-data/alfa_toy.gtf	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-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";
--- a/alfa/alfa/alfa/test-data/alfa_toy.stranded.index	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#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
--- a/alfa/alfa/alfa/test-data/alfa_toy.unstranded.index	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-#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
--- a/alfa/alfa/alfa/tool-data/alfa_indexes.loc.sample	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-#<species>	<version>	<release>	<value>	<dbkey>	<name>	<prefix>
-#Dictyostelium_discoideum	dicty_2	7	Dictyostelium_discoideum_dicty_2_7	Dictyostelium_discoideum_dicty_2_7	Dictyostelium_discoideum: dicty_2 (release 7)	<path_to_dicty_indexes_dir>
Binary file alfa/test-data/alfa_toy.bam has changed
--- a/alfa/test-data/alfa_toy.bedgraph	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-Chr1	149	199	2
-Chr1	299	349	1
-Chr1	499	549	6
-Chr1	1099	1149	1
--- a/alfa/test-data/alfa_toy.categories_counts	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-#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
--- a/alfa/test-data/alfa_toy.gtf	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-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";
--- a/alfa/test-data/alfa_toy.stranded.index	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-#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
--- a/alfa/test-data/alfa_toy.unstranded.index	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-#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
--- a/alfa/tool-data/alfa_indexes.loc.sample	Thu Dec 21 09:40:18 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-#<species>	<version>	<release>	<value>	<dbkey>	<name>	<prefix>
-#Dictyostelium_discoideum	dicty_2	7	Dictyostelium_discoideum_dicty_2_7	Dictyostelium_discoideum_dicty_2_7	Dictyostelium_discoideum: dicty_2 (release 7)	<path_to_dicty_indexes_dir>