Mercurial > repos > charles-bernard > alfa
changeset 17:e3d439570972 draft
Uploaded
| author | charles-bernard |
|---|---|
| date | Tue, 11 Oct 2016 09:15:14 -0400 |
| parents | cbb0a78e61e8 |
| children | a1e2ab10b317 |
| files | test-data/alfa_toy-Biofeatures Distribution.pdf test-data/alfa_toy.bam test-data/alfa_toy.bedgraph test-data/alfa_toy.categories_counts test-data/alfa_toy.gtf test-data/alfa_toy.stranded.index test-data/alfa_toy.unstranded.index tool-data/alfa_genomes_indexes.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 9 files changed, 32 insertions(+), 12 deletions(-) [+] |
line wrap: on
line diff
--- /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
--- /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
--- /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";
--- /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
--- /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
--- 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
--- 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