Merge pull request #47 from databio/dev

Major updates to pipeline use

.gitignore

@@ -1,3 +1,27 @@
+# General
+*.pyc
+.~lock*
+
+# Tests
+.cache/
+*peppro_test*
+
+# MkDocs files
+site/
+
+# Jekyll files
+jekyll/
+_site
+.DS_store
+.jekyll
+.bundle
+.sass-cache
+_site/
+/_site/
+.sass-cache/
+.jekyll-metadata
+
+# Annotation files
 # ignore local annotation files
 anno/hg19_annotations.bed.gz
 anno/hg19_annotations.bed
@@ -7,3 +31,4 @@ anno/mm10_annotations.bed.gz
 anno/mm10_annotations.bed
 anno/mm9_annotations.bed.gz
 anno/mm9_annotations.bed
+

BiocProject/PEPPRO_BiocProject.Rmd

@@ -0,0 +1,55 @@
+---
+title: "PEPPRO BiocProject"
+author: "Jason Smith"
+date: "`r Sys.Date()`"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{PEPPRO BiocProject}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+
+```{r setup, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+# Introduction
+
+Before you start see the [Getting started with `BiocProject` vignette](http://code.databio.org/BiocProject/articles/vignette1getStarted.html) for the basic `BiocProject` information and installation instructions and [`PEPPRO` website](http://peppro.databio.org) for information regarding this nascent RNA profiling pipeline.
+
+`BiocProject` provides a straigtforward method to read in pipeline outputs as listed in the `outputs` section of its [pipeline interface](http://code.databio.org/looper/pipeline-interface/). 
+
+__With a single line of code you can read all the indicated results and your project metadata.__
+
+# Read the results of `PEPPRO` run
+
+The function shown below reads in the gene count `BED` files from the `output` section specified in the [`PEPPRO` pipeline interface](https://github.com/databio/peppro/blob/master/pipeline_interface.yaml).
+
+The way the output files are read is defined in a [function](https://github.com/databio/peppro/blob/master/BiocProject/readPepproGeneCounts.R) supplied by the `PEPPRO` developers. The function listed in `bioconductor` section of `PEPPRO` pipeline interface file is identified by `BiocProject` function, sourced and automatically executed on samples matching the protocols bound to the pipeline specified as an argument in [`outputsByPipeline`](http://code.databio.org/BiocProject/reference/outputsByPipeline.html) function.
+
+## Get the project config
+
+```{r echo=T, message=FALSE}
+library(BiocProject)
+ProjectConfig = "peppro_da.yaml"
+```
+
+## Run the `BiocProject` function
+
+```{r}
+bp = BiocProject(ProjectConfig)
+```
+
+As you can see in the message above, the `readPepproGeneCounts` function was sourced from the file indicated in the `PEPPRO` pipeline interface.
+
+## Browse the results
+
+The read data is conveninetly stored in a `List` object with ([`pepr::Project`](http://code.databio.org/pepr/reference/Project-class.html) object in its metadata slot:
+
+```{r}
+bp
+```

BiocProject/peppro_da.csv

@@ -0,0 +1,7 @@
+sample_name,toggle,protocol,organism,read_type,umi_status,umi_length,data_source,read1,read2,srr,experiment,geo,Assay Type,AvgSpotLen,Bases,BioProject,BioSample,Bytes,Cell_Line,Cell_type,Center Name,Consent,DATASTORE filetype,DATASTORE provider,DATASTORE region,Instrument,LibraryLayout,LibrarySelection,LibrarySource,Organism,Platform,ReleaseDate,Sample Name,source_name,SRA Study,treatment
+H9_DMSO_rep1,1,PRO,human,PAIRED,true_8,8,SRA,PE1,PE2,SRR10669536,SRX7348011,GSM4214080,OTHER,83,4066110724,PRJNA594951,SAMN13541464,1576539216,H9,embryonic stem cells,GEO,public,"fastq,sra","s3,ncbi,gs","s3.us-east-1,gs.US,ncbi.public",NextSeq 500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,2019-12-13T00:00:00Z,GSM4214080,H9 cells,SRP236879,control
+H9_DMSO_rep2,1,PRO,human,PAIRED,true_8,8,SRA,PE1,PE2,SRR10669537,SRX7348012,GSM4214081,OTHER,83,4824187397,PRJNA594951,SAMN13541463,1851708346,H9,embryonic stem cells,GEO,public,"sra,fastq","gs,s3,ncbi","gs.US,s3.us-east-1,ncbi.public",NextSeq 500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,2019-12-13T00:00:00Z,GSM4214081,H9 cells,SRP236879,control
+H9_DMSO_rep3,1,PRO,human,PAIRED,true_8,8,SRA,PE1,PE2,SRR10669538,SRX7348013,GSM4214082,OTHER,83,3857336412,PRJNA594951,SAMN13541462,1508923353,H9,embryonic stem cells,GEO,public,"sra,fastq","s3,ncbi,gs","gs.US,s3.us-east-1,ncbi.public",NextSeq 500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,2019-12-13T00:00:00Z,GSM4214082,H9 cells,SRP236879,control
+H9_200nM_romidepsin_rep1,1,PRO,human,PAIRED,true_8,8,SRA,PE1,PE2,SRR10669539,SRX7348014,GSM4214083,OTHER,83,4636791999,PRJNA594951,SAMN13541471,1798846852,H9,embryonic stem cells,GEO,public,"fastq,sra","gs,ncbi,s3","gs.US,ncbi.public,s3.us-east-1",NextSeq 500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,2019-12-13T00:00:00Z,GSM4214083,H9 cells,SRP236879,60 minutes 200nM romidepsin
+H9_200nM_romidepsin_rep2,1,PRO,human,PAIRED,true_8,8,SRA,PE1,PE2,SRR10669540,SRX7348015,GSM4214084,OTHER,82,4730726832,PRJNA594951,SAMN13541470,1833437275,H9,embryonic stem cells,GEO,public,"fastq,sra","ncbi,gs,s3","gs.US,ncbi.public,s3.us-east-1",NextSeq 500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,2019-12-13T00:00:00Z,GSM4214084,H9 cells,SRP236879,60 minutes 200nM romidepsin
+H9_200nM_romidepsin_rep3,1,PRO,human,PAIRED,true_8,8,SRA,PE1,PE2,SRR10669541,SRX7348016,GSM4214085,OTHER,83,5015008131,PRJNA594951,SAMN13541469,1922230177,H9,embryonic stem cells,GEO,public,"fastq,sra","s3,gs,ncbi","ncbi.public,gs.US,s3.us-east-1",NextSeq 500,PAIRED,other,TRANSCRIPTOMIC,Homo sapiens,ILLUMINA,2019-12-13T00:00:00Z,GSM4214085,H9 cells,SRP236879,60 minutes 200nM romidepsin

BiocProject/peppro_da.yaml

@@ -0,0 +1,27 @@
+# Run PEPPRO paper differential analysis samples through PEPPRO
+name: PEPPRO
+
+metadata:
+  sample_table: "peppro_da.csv"
+  output_dir: "$PROCESSED/peppro/paper/da"
+  pipeline_interfaces: "$CODE/peppro/pipeline_interface.yaml" 
+bioconductor:
+  readFunName: readPepproGeneCounts
+  readFunPath: readPepproGeneCounts.R
+
+derived_columns: [read1, read2]
+
+data_sources:
+  PE1: "${SRAFQ}/{srr}_1.fastq.gz"
+  PE2: "${SRAFQ}/{srr}_2.fastq.gz"
+
+implied_columns:
+  organism:
+    human:
+      genome: hg38
+      prealignments: human_rDNA
+      max_len: -1
+  umi_status:
+    true_8:
+      umi_len: 8
+

BiocProject/readPepproGeneCounts.R

@@ -0,0 +1,31 @@
+readPepproGeneCounts = function(project) {
+    cwd            <- getwd()
+    project_dir    <- pepr::config(project)$metadata$output_dir
+    sample_names   <- pepr::samples(project)$sample_name
+    genomes        <- as.list(pepr::samples(project)$genome)
+    names(genomes) <- sample_names
+    paths          <- vector("list", length(sample_names))
+    names(paths)   <- sample_names
+
+    for (sample in sample_names) {
+        paths[[sample]] <- paste(project_dir, 'results_pipeline', sample,
+                                 paste0('signal_', genomes[[sample]]),
+                                 paste0(sample, "_gene_coverage.bed"), sep="/")
+    }
+
+    result <- lapply(paths, function(x){
+        #message(paste0("x: ", x))
+        if (file.exists(x)) {
+            df <- fread(x)
+            colnames(df) <- c('chr', 'start', 'end', 'geneName',
+                              'score', 'strand', 'count')
+            gr <- GenomicRanges::GRanges(df) 
+        } else {
+            gr <- GenomicRanges::GRanges() 
+        }
+    })
+
+    setwd(cwd)
+    #names(result) <- sample_names
+    return(GenomicRanges::GRangesList(Filter(length, result)))
+}

PEPPROr/DESCRIPTION

@@ -1,6 +1,6 @@
 Package: PEPPROr
 Title: Functions and libraries to analyze pro-seq (or gro-seq) data
-Version: 0.0.1.0000
+Version: 0.0.2.0000
 Authors@R: person("Jason", "Smith", email = "jasonsmith@virginia.edu", role = c("aut", "cre"))
 Maintainer: Jason Smith <jasonsmith@virginia.edu>
 Description: Installs required libraries to calculate the fraction of reads in features, to plot library complexity curves, TSS enrichments, and fragment length distributions. 

PEPPROr/NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(plotCutadapt)
+export(plotAdapt)
 export(plotPI)
 export(mRNAcontamination)
 export(plotFRiF)