Test data
inst/extdata/oa/, tracked with DVC on a public R2 bucket. dvc pull in a clone, or from R:
View input files
indir <- system.file("extdata/oa", package = "tidywigits")
dir_tree(indir, invert = TRUE, glob = "*.dvc")
#> /home/runner/miniconda3/envs/pkgdown_env/lib/R/library/tidywigits/extdata/oa
#> ├── alignments
#> │ ├── sample1.duplicate_freq.tsv
#> │ ├── sample1.md.metrics
#> │ └── sample1.redux.duplicate_freq.tsv
#> ├── amber
#> │ ├── amber.version
#> │ ├── sample1.amber.baf.pcf
#> │ ├── sample1.amber.contamination.tsv
#> │ ├── sample1.amber.homozygousregion.tsv
#> │ ├── sample1.amber.qc
#> │ └── v4.2
#> │ └── sample1.amber.baf.pcf
#> ├── bamtools
#> │ ├── sample1.bam_metric.coverage.tsv
#> │ ├── sample1.bam_metric.exon_coverage.tsv
#> │ ├── sample1.bam_metric.flag_counts.tsv
#> │ ├── sample1.bam_metric.frag_length.tsv
#> │ ├── sample1.bam_metric.gene_coverage.tsv
#> │ ├── sample1.bam_metric.partition_stats.tsv
#> │ ├── sample1.bam_metric.summary.tsv
#> │ └── v1.4.2
#> │ ├── sample1.bam_metric.exon_medians.tsv
#> │ ├── sample1.bam_metric.gene_coverage.tsv
#> │ ├── sample1.bam_metric.summary.tsv
#> │ └── sample1.wgsmetrics
#> ├── chord
#> │ ├── sample1.chord.mutation_contexts.tsv
#> │ └── sample1.chord.prediction.tsv
#> ├── cider
#> │ ├── sample1.cider.alignment_match.tsv.gz
#> │ ├── sample1.cider.locus_stats.tsv
#> │ ├── sample1.cider.vdj.tsv.gz
#> │ └── v1.0.0
#> │ ├── sample1.cider.blastn_match.tsv.gz
#> │ └── sample1.cider.vdj.tsv.gz
#> ├── cobalt
#> │ ├── cobalt.version
#> │ ├── sample1.cobalt.gc.median.tsv
#> │ ├── sample1.cobalt.ratio.median.tsv
#> │ ├── sample1.cobalt.ratio.pcf
#> │ └── v2.0
#> │ └── sample1.cobalt.ratio.pcf
#> ├── cuppa
#> │ ├── sample1.cup.data.csv
#> │ ├── sample1.cuppa.pred_summ.tsv
#> │ ├── sample1.cuppa.vis_data.tsv
#> │ ├── sample1.cuppa_data.tsv.gz
#> │ └── v1.4
#> │ └── sample1.cup.data.csv
#> ├── esvee
#> │ ├── sample1.esvee.alignment.tsv
#> │ ├── sample1.esvee.assembly.tsv
#> │ ├── sample1.esvee.breakend.tsv
#> │ ├── sample1.esvee.phased_assembly.tsv
#> │ ├── sample1.esvee.prep.disc_stats.tsv
#> │ ├── sample1.esvee.prep.fragment_length.tsv
#> │ ├── sample1.esvee.prep.junction.tsv
#> │ └── v1.0
#> │ ├── sample1.esvee.breakend.tsv
#> │ └── sample1.esvee.prep.junction.tsv
#> ├── flagstats
#> │ └── sample1.flagstat
#> ├── isofox
#> │ ├── sample1.isf.alt_splice_junc.csv
#> │ ├── sample1.isf.alt_splice_junc.tsv
#> │ ├── sample1.isf.alt_splice_junc_unfiltered.tsv
#> │ ├── sample1.isf.fusions.csv
#> │ ├── sample1.isf.fusions.tsv
#> │ ├── sample1.isf.gene_collection.csv
#> │ ├── sample1.isf.gene_collection.tsv
#> │ ├── sample1.isf.gene_data.csv
#> │ ├── sample1.isf.gene_data.tsv
#> │ ├── sample1.isf.pass_fusions.csv
#> │ ├── sample1.isf.pass_fusions.tsv
#> │ ├── sample1.isf.retained_intron.csv
#> │ ├── sample1.isf.summary.csv
#> │ ├── sample1.isf.summary.tsv
#> │ ├── sample1.isf.transcript_data.csv
#> │ └── sample1.isf.transcript_data.tsv
#> ├── lilac
#> │ ├── sample1.lilac.qc.tsv
#> │ ├── sample1.lilac.tsv
#> │ └── v1.7.1
#> │ ├── sample1.lilac.qc.tsv
#> │ └── sample1.lilac.tsv
#> ├── linx
#> │ ├── germline_annotations
#> │ │ ├── linx.version
#> │ │ ├── sample1.linx.germline.breakend.tsv
#> │ │ ├── sample1.linx.germline.clusters.tsv
#> │ │ ├── sample1.linx.germline.disruption.tsv
#> │ │ ├── sample1.linx.germline.driver.catalog.tsv
#> │ │ ├── sample1.linx.germline.links.tsv
#> │ │ └── sample1.linx.germline.svs.tsv
#> │ ├── somatic_annotations
#> │ │ ├── linx.version
#> │ │ ├── sample1.linx.breakend.tsv
#> │ │ ├── sample1.linx.clusters.tsv
#> │ │ ├── sample1.linx.driver.catalog.tsv
#> │ │ ├── sample1.linx.drivers.tsv
#> │ │ ├── sample1.linx.fusion.tsv
#> │ │ ├── sample1.linx.links.tsv
#> │ │ ├── sample1.linx.neoepitope.tsv
#> │ │ ├── sample1.linx.svs.tsv
#> │ │ ├── sample1.linx.vis_copy_number.tsv
#> │ │ ├── sample1.linx.vis_fusion.tsv
#> │ │ ├── sample1.linx.vis_gene_exon.tsv
#> │ │ ├── sample1.linx.vis_protein_domain.tsv
#> │ │ ├── sample1.linx.vis_segments.tsv
#> │ │ └── sample1.linx.vis_sv_data.tsv
#> │ ├── v1.25
#> │ │ ├── germline_ann
#> │ │ │ ├── linx.version
#> │ │ │ └── sample1.linx.germline.breakend.tsv
#> │ │ └── somatic_ann
#> │ │ ├── linx.version
#> │ │ ├── sample1.linx.breakend.tsv
#> │ │ ├── sample1.linx.vis_copy_number.tsv
#> │ │ ├── sample1.linx.vis_fusion.tsv
#> │ │ ├── sample1.linx.vis_gene_exon.tsv
#> │ │ ├── sample1.linx.vis_protein_domain.tsv
#> │ │ ├── sample1.linx.vis_segments.tsv
#> │ │ └── sample1.linx.vis_sv_data.tsv
#> │ └── v2.1
#> │ ├── germline_ann
#> │ │ ├── sample1.linx.germline.breakend.tsv
#> │ │ ├── sample1.linx.germline.driver.catalog.tsv
#> │ │ └── sample1.linx.germline.svs.tsv
#> │ └── somatic_ann
#> │ ├── sample1.linx.breakend.tsv
#> │ ├── sample1.linx.driver.catalog.tsv
#> │ ├── sample1.linx.fusion.tsv
#> │ └── sample1.linx.svs.tsv
#> ├── neo
#> │ ├── sample1.isf.neoepitope.tsv
#> │ ├── sample1.neo.neo_data.tsv
#> │ ├── sample1.neo.neoepitope.tsv
#> │ └── sample1.neo.peptide_scores.tsv
#> ├── peach
#> │ ├── sample1.peach.events.tsv
#> │ ├── sample1.peach.gene.events.tsv
#> │ ├── sample1.peach.haplotypes.all.tsv
#> │ ├── sample1.peach.haplotypes.best.tsv
#> │ └── sample1.peach.qc.tsv
#> ├── purple
#> │ ├── purple.version
#> │ ├── sample1.purple.chromosome_arm.tsv
#> │ ├── sample1.purple.cnv.gene.tsv
#> │ ├── sample1.purple.cnv.somatic.tsv
#> │ ├── sample1.purple.driver.catalog.germline.tsv
#> │ ├── sample1.purple.driver.catalog.somatic.tsv
#> │ ├── sample1.purple.germline_amp_del.tsv
#> │ ├── sample1.purple.purity.range.tsv
#> │ ├── sample1.purple.purity.tsv
#> │ ├── sample1.purple.qc
#> │ ├── sample1.purple.somatic.clonality.tsv
#> │ ├── sample1.purple.somatic.hist.tsv
#> │ ├── v4.0
#> │ │ ├── purple.version
#> │ │ ├── sample1.purple.cnv.gene.tsv
#> │ │ └── sample1.purple.qc
#> │ └── v4.2
#> │ ├── sample1.purple.cnv.gene.tsv
#> │ ├── sample1.purple.driver.catalog.germline.tsv
#> │ ├── sample1.purple.driver.catalog.somatic.tsv
#> │ └── sample1.purple.germline.deletion.tsv
#> ├── qsee
#> │ ├── sample1.qsee.status.tsv.gz
#> │ └── sample1.qsee.vis.data.tsv.gz
#> ├── sage
#> │ ├── germline
#> │ │ ├── sample1.sage.bqr.tsv
#> │ │ ├── sample2.sage.bqr.tsv
#> │ │ ├── sample2.sage.exon.medians.tsv
#> │ │ └── sample2.sage.gene.coverage.tsv
#> │ ├── somatic
#> │ │ ├── sample1.sage.bqr.tsv
#> │ │ ├── sample1.sage.exon.medians.tsv
#> │ │ ├── sample1.sage.gene.coverage.tsv
#> │ │ └── sample2.sage.bqr.tsv
#> │ └── v3.4.4
#> │ └── sample1.sage.bqr.tsv
#> ├── sigs
#> │ ├── sample1.sig.allocation.tsv
#> │ └── sample1.sig.snv_counts.csv
#> ├── teal
#> │ ├── sample1.teal.breakend.tsv.gz
#> │ └── sample1.teal.tellength.tsv
#> ├── virusbreakend
#> │ └── sample1.virusbreakend.vcf.summary.tsv
#> └── virusinterpreter
#> └── sample1.virus.annotated.tsv
Each tool has its own R6 class. run() parses, tidies and writes in one step:
outdir <- file.path(tempdir(), "qs_ppl")
Purple$new(file.path(indir, "purple"))$run(
output_dir = outdir,
format = "parquet",
input_id = "sample1_id"
)
list.files(outdir, pattern = "\\.parquet$")
#> [1] "metadata_purple.parquet"
#> [2] "sample1_2_purple_cnvgenetsv.parquet"
#> [3] "sample1_2_purple_qc.parquet"
#> [4] "sample1_3_purple_cnvgenetsv.parquet"
#> [5] "sample1_germline_2_purple_drivercatalog.parquet"
#> [6] "sample1_germline_purple_drivercatalog.parquet"
#> [7] "sample1_purple_chromarm.parquet"
#> [8] "sample1_purple_cnvgenetsv.parquet"
#> [9] "sample1_purple_cnvsomtsv.parquet"
#> [10] "sample1_purple_germampdel.parquet"
#> [11] "sample1_purple_germdeltsv.parquet"
#> [12] "sample1_purple_purityrange.parquet"
#> [13] "sample1_purple_puritytsv.parquet"
#> [14] "sample1_purple_qc.parquet"
#> [15] "sample1_purple_somclonality.parquet"
#> [16] "sample1_purple_somhist.parquet"
#> [17] "sample1_somatic_2_purple_drivercatalog.parquet"
#> [18] "sample1_somatic_purple_drivercatalog.parquet"
#> [19] "version_2_purple_version.parquet"
#> [20] "version_purple_version.parquet"
File naming
{prefix}_{tool}_{table}.parquet, prefix from input filename (sample1). See Output Naming.
Reading a table back
qc <- read_parquet(file.path(outdir, "sample1_purple_qc.parquet"))
qc |> str()
#> tibble [1 × 15] (S3: tbl_df/tbl/data.frame)
#> $ input_id : chr "sample1_id"
#> $ qc_status : chr "PASS"
#> $ method : chr "NORMAL"
#> $ cn_segments : int 472
#> $ cn_segments_unsupported: int 5
#> $ purity : num 1
#> $ gender_amber : chr "FEMALE"
#> $ gender_cobalt : chr "FEMALE"
#> $ deleted_genes : int 0
#> $ contamination : num 0
#> $ germline_aberrations : chr "NONE"
#> $ mean_depth_amber : num 79
#> $ loh_percent : num 0.027
#> $ tinc_level : num 0
#> $ chimerism_percent : num 0
#> - attr(*, "file_version")= chr "latest"
Output - Full WiGiTS run
Wigits runs all supported tools on a parent directory:
outdir_w <- file.path(tempdir(), "qs_wigits")
w <- Wigits$new(indir)
w$run(
output_dir = outdir_w,
format = "parquet"
)
list.files(outdir_w, pattern = "\\.parquet$") |> sort() |> str()
#> chr [1:161] "metadata.parquet" "sample1_2_alignments_dupfreq.parquet" ...
ID columns
Optional, off by default:
input_id = "x" |
input_id |
sample or run identifier you supply |
output_id = "x" |
output_id |
processing run identifier you supply |
prefix_include = TRUE |
input_prefix |
filename prefix extracted from input files |
outdir_id <- file.path(tempdir(), "qs_ppl_id")
Purple$new(file.path(indir, "purple"))$run(
output_dir = outdir_id,
format = "parquet",
input_id = "sample1",
output_id = "out1",
prefix_include = TRUE
)
read_parquet(file.path(outdir_id, "sample1_purple_qc.parquet"))
#> # A tibble: 1 × 17
#> input_id input_prefix output_id qc_status method cn_segments cn_segments_unsupported
#> * <chr> <chr> <chr> <chr> <chr> <int> <int>
#> 1 sample1 sample1 out1 PASS NORMAL 472 5
#> # ℹ 10 more variables: purity <dbl>, gender_amber <chr>, gender_cobalt <chr>,
#> # deleted_genes <int>, contamination <dbl>, germline_aberrations <chr>,
#> # mean_depth_amber <dbl>, loh_percent <dbl>, tinc_level <dbl>, chimerism_percent <dbl>
Every run() also writes metadata (input/output dirs, IDs, R package versions): metadata.parquet for Wigits, metadata_<tool>.parquet for a single tool.
read_parquet(file.path(outdir_w, "metadata.parquet")) |> str()
#> tibble [1 × 6] (S3: tbl_df/tbl/data.frame)
#> $ input_id : chr NA
#> $ output_id : chr NA
#> $ input_dirs : list<character> [1:1]
#> ..$ : chr "/home/runner/miniconda3/envs/pkgdown_env/lib/R/library/tidywigits/extdata/oa"
#> ..@ ptype: chr(0)
#> $ output_dir : chr "/tmp/RtmpS5SbG6/qs_wigits"
#> $ pkg_versions: list<
#> tbl_df<
#> name : character
#> version: character
#> >
#> > [1:1]
#> ..$ : tibble [2 × 2] (S3: tbl_df/tbl/data.frame)
#> .. ..$ name : chr [1:2] "nemo" "tidywigits"
#> .. ..$ version: chr [1:2] "0.2.0.9000" "0.2.2"
#> ..@ ptype: tibble [0 × 2] (S3: tbl_df/tbl/data.frame)
#> .. ..$ name : chr(0)
#> .. ..$ version: chr(0)
#> $ files : list<
#> tbl_df<
#> tbl : character
#> prefix: character
#> fout : character
#> fin : character
#> >
#> > [1:1]
#> ..$ : tibble [160 × 4] (S3: tbl_df/tbl/data.frame)
#> .. ..$ tbl : chr [1:160] "alignments_dupfreq" "alignments_markdup" "alignments_dupfreq" "amber_version" ...
#> .. ..$ prefix: chr [1:160] "sample1" "sample1" "sample1_2" "version" ...
#> .. ..$ fout : chr [1:160] "sample1_alignments_dupfreq.parquet" "sample1_alignments_markdup.parquet" "sample1_2_alignments_dupfreq.parquet" "version_amber_version.parquet" ...
#> .. ..$ fin : chr [1:160] "/home/runner/miniconda3/envs/pkgdown_env/lib/R/library/tidywigits/extdata/oa/alignments/sample1.duplicate_freq.tsv" "/home/runner/miniconda3/envs/pkgdown_env/lib/R/library/tidywigits/extdata/oa/alignments/sample1.md.metrics" "/home/runner/miniconda3/envs/pkgdown_env/lib/R/library/tidywigits/extdata/oa/alignments/sample1.redux.duplicate_freq.tsv" "/home/runner/miniconda3/envs/pkgdown_env/lib/R/library/tidywigits/extdata/oa/amber/amber.version" ...
#> ..@ ptype: tibble [0 × 4] (S3: tbl_df/tbl/data.frame)
#> .. ..$ tbl : chr(0)
#> .. ..$ prefix: chr(0)
#> .. ..$ fout : chr(0)
#> .. ..$ fin : chr(0)
