# HG changeset patch # User charles-bernard # Date 1513868229 18000 # Node ID d88413b718de20d44b657352269141ed56cea87c # Parent 5adde3d05247070e76a7ff4219dd45fa63aa540d Uploaded diff -r 5adde3d05247 -r d88413b718de alfa/alfa/alfa/test-data/alfa_toy-Biofeatures Distribution.pdf Binary file alfa/alfa/alfa/test-data/alfa_toy-Biofeatures Distribution.pdf has changed diff -r 5adde3d05247 -r d88413b718de alfa/alfa/alfa/test-data/alfa_toy.bam Binary file alfa/alfa/alfa/test-data/alfa_toy.bam has changed diff -r 5adde3d05247 -r d88413b718de alfa/alfa/alfa/test-data/alfa_toy.bedgraph --- 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 diff -r 5adde3d05247 -r d88413b718de alfa/alfa/alfa/test-data/alfa_toy.categories_counts --- 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 diff -r 5adde3d05247 -r d88413b718de alfa/alfa/alfa/test-data/alfa_toy.gtf --- 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"; diff -r 5adde3d05247 -r d88413b718de alfa/alfa/alfa/test-data/alfa_toy.stranded.index --- 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 diff -r 5adde3d05247 -r d88413b718de alfa/alfa/alfa/test-data/alfa_toy.unstranded.index --- 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 diff -r 5adde3d05247 -r d88413b718de alfa/alfa/alfa/tool-data/alfa_indexes.loc.sample --- 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 @@ -# -#Dictyostelium_discoideum dicty_2 7 Dictyostelium_discoideum_dicty_2_7 Dictyostelium_discoideum_dicty_2_7 Dictyostelium_discoideum: dicty_2 (release 7) diff -r 5adde3d05247 -r d88413b718de alfa/test-data/alfa_toy.bam Binary file alfa/test-data/alfa_toy.bam has changed diff -r 5adde3d05247 -r d88413b718de alfa/test-data/alfa_toy.bedgraph --- 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 diff -r 5adde3d05247 -r d88413b718de alfa/test-data/alfa_toy.categories_counts --- 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 diff -r 5adde3d05247 -r d88413b718de alfa/test-data/alfa_toy.gtf --- 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"; diff -r 5adde3d05247 -r d88413b718de alfa/test-data/alfa_toy.stranded.index --- 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 diff -r 5adde3d05247 -r d88413b718de alfa/test-data/alfa_toy.unstranded.index --- 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 diff -r 5adde3d05247 -r d88413b718de alfa/tool-data/alfa_indexes.loc.sample --- 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 @@ -# -#Dictyostelium_discoideum dicty_2 7 Dictyostelium_discoideum_dicty_2_7 Dictyostelium_discoideum_dicty_2_7 Dictyostelium_discoideum: dicty_2 (release 7)