John Kerl johnkerl
johnkerl
/ show-new.txt
Created
January 22, 2022 00:55
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| SCHEMA | |
| tiledb_array_schema( | |
| domain=tiledb_domain(c(tiledb_dim(name="gene_id", domain=c(NULL,NULL), tile=NULL, type="ASCII"), tiledb_dim(name="sample", domain=c(NULL,NULL), tile=NULL, type="ASCII"))), | |
| attrs=c(tiledb_attr(name="tpm", type="FLOAT64", ncells=1, nullable=FALSE, filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",1))))), | |
| cell_order="ROW_MAJOR", tile_order="ROW_MAJOR", capacity=18000, sparse=TRUE, allows_dups=FALSE, | |
| coords_filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",-1))), | |
| offsets_filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("POSITIVE_DELTA"),"POSITIVE_DELTA_MAX_WINDOW",1024)), tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",1)))) | |
| FILTER_LIST | |
| $coords |
johnkerl
/ show-old.txt
Created
January 22, 2022 00:54
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| SCHEMA | |
| - Array type: sparse | |
| - Cell order: ROW_MAJOR | |
| - Tile order: ROW_MAJOR | |
| - Capacity: 18000 | |
| - Allows duplicates: FALSE | |
| - Coordinates filters: 1 | |
| > ZSTD: COMPRESSION_LEVEL=-1 | |
| - Offsets filters: 2 | |
| > POSITIVE_DELTA: POSITIVE_DELTA_MAX_WINDOW=1024 |
johnkerl
/ test-show.r
Created
January 22, 2022 00:54
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| #!/usr/bin/env Rscript | |
| library(tiledb) | |
| uri <- "tiledb://TileDB-Inc/gtex-analysis-rnaseqc-gene-tpm" | |
| arr <- tiledb_array(uri, query_type="READ", as.data.frame=TRUE) | |
| sch <- schema(arr); | |
| cat("SCHEMA\n") | |
| show(sch) |
johnkerl
/ show-new.txt
Created
January 22, 2022 00:44
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| SCHEMA | |
| tiledb_array_schema( | |
| domain=tiledb_domain(c(tiledb_dim(name="gene_id", domain=c(NULL,NULL), tile=NULL, type="ASCII"), tiledb_dim(name="sample", domain=c(NULL,NULL), tile=NULL, type="ASCII"))), | |
| attrs=c(tiledb_attr(name="tpm", type="FLOAT64", ncells=1, nullable=FALSE, filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",1))))), | |
| cell_order="ROW_MAJOR", tile_order="ROW_MAJOR", capacity=18000, sparse=TRUE, allows_dups=FALSE, | |
| coords_filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",-1))), | |
| offsets_filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("POSITIVE_DELTA"),"POSITIVE_DELTA_MAX_WINDOW",1024)), tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",1)))) | |
| FILTER_LIST | |
| $coords |
johnkerl
/ show-new.txt
Created
January 22, 2022 00:42
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| johnkerl@ip-192-168-1-183[prod][r]$ test-show.r | |
| SCHEMA | |
| tiledb_array_schema( | |
| domain=tiledb_domain(c(tiledb_dim(name="gene_id", domain=c(NULL,NULL), tile=NULL, type="ASCII"), tiledb_dim(name="sample", domain=c(NULL,NULL), tile=NULL, type="ASCII"))), | |
| attrs=c(tiledb_attr(name="tpm", type="FLOAT64", ncells=1, nullable=FALSE, filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",1))))), | |
| cell_order="ROW_MAJOR", tile_order="ROW_MAJOR", capacity=18000, sparse=TRUE, allows_dups=FALSE, | |
| coords_filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",-1))), | |
| offsets_filter_list=tiledb_filter_list(c(tiledb_filter_set_option(tiledb_filter("POSITIVE_DELTA"),"POSITIVE_DELTA_MAX_WINDOW",1024)), tiledb_filter_set_option(tiledb_filter("ZSTD"),"COMPRESSION_LEVEL",1))), | |
| ) |
johnkerl
/ show-old.txt
Created
January 22, 2022 00:42
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| johnkerl@ip-192-168-1-183[prod][r]$ ./test-show.r | |
| SCHEMA | |
| - Array type: sparse | |
| - Cell order: ROW_MAJOR | |
| - Tile order: ROW_MAJOR | |
| - Capacity: 18000 | |
| - Allows duplicates: FALSE | |
| - Coordinates filters: 1 | |
| > ZSTD: COMPRESSION_LEVEL=-1 | |
| - Offsets filters: 2 |
johnkerl
/ test-show.r
Created
January 22, 2022 00:41
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| #!/usr/bin/env Rscript | |
| library(tiledb) | |
| uri <- "tiledb://TileDB-Inc/gtex-analysis-rnaseqc-gene-tpm" | |
| arr <- tiledb_array(uri, query_type="READ", as.data.frame=TRUE) | |
| sch <- schema(arr); | |
| cat("SCHEMA\n") | |
| show(sch) |
johnkerl
/ gist:b381ad9bc2003acc94a114cce629a921
Created
January 13, 2022 13:55
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| $ cat deslurm2.mlrsh | |
| #!/usr/bin/env mlr -s | |
| --csv | |
| put ' | |
| func deslurm(str s): num { | |
| # example "5-18:53:20" | |
| fields = unformat("{}-{}:{}:{}", s); | |
| days = fields[1]; | |
| hours = fields[2]; |
johnkerl
/ gist:0629596cd53cd14404bb51cfd1481a28
Created
January 13, 2022 13:53
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| $ cat deslurm.mlrsh | |
| #!/usr/bin/env mlr -s | |
| --csv put -f deslurm2.mlr -e '$y = deslurm($x)' -e '$z=sec2dhms($y)' | |
| $ deslurm.mlrsh test.csv | |
| x,y,z | |
| 5-18:53:20,500000,5d18h53m20s |
johnkerl
/ deslurm examples
Created
January 13, 2022 13:50
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| $ cat test.csv | |
| x | |
| 5-18:53:20 | |
| $ cat deslurm.mlr | |
| func deslurm(str s): num { | |
| # example "5-18:53:20" | |
| t = splita(s, "-"); | |
| u = splita(t[2], ":"); | |
| days = t[1]; |