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merged devel into c++ find_isoform version
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,65 @@ | ||
| #' BLAZE Assign reads to cell barcodes. | ||
| #' | ||
| #' @description | ||
| #' Uses BLAZE to generate barcode list and assign reads to cell barcodes. | ||
| #' Uses default options for BLAZE, see BLAZE documentation for details (https://github.com/shimlab/BLAZE). | ||
| #' | ||
| #' @param blaze_config List, additional BLAZE configuration parameters | ||
| #' @param fq_in File path to the fastq file used as a query sequence file | ||
| #' | ||
| #' @return a \code{data.frame} summarising the reads aligned | ||
| #' | ||
| #' @importFrom parallel detectCores | ||
| #' @export | ||
| #' @examples | ||
| #' temp_path <- tempfile() | ||
| #' bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE) | ||
| #' bc_list_10x_url <- 'https://github.com/shimlab/BLAZE/blob/main/10X_bc/3M-february-2018.zip' | ||
| #' bc_list_10x <- bfc[[names(BiocFileCache::bfcadd(bfc, 'bc_list_10x', bc_list_10x_url))]] | ||
| #' fastq1_url <- 'https://raw.githubusercontent.com/shimlab/BLAZE/main/test/data/FAR20033_pass_51e510db_100.fastq' | ||
| #' fastq1 <- bfc[[names(BiocFileCache::bfcadd(bfc, 'Fastq1', fastq1_url))]] | ||
| #' outdir <- tempfile() | ||
| #' dir.create(outdir) | ||
| #' config = jsonlite::fromJSON(system.file('extdata/blaze_flames.json', package = 'FLAMES')) | ||
| #' config$blaze_parameters['output-prefix'] <- outdir | ||
| #' blaze(config$blaze_parameters, fastq1) | ||
| #' @importFrom reticulate import_from_path dict | ||
| #' @export | ||
| blaze <- function(blaze_config, fq_in) { | ||
|
|
||
| # command line arguments for blaze | ||
| blaze_argv <- paste("") | ||
|
|
||
| if (blaze_config['overwrite'] == TRUE) { | ||
| blaze_argv <- paste(blaze_argv, '--overwrite ') | ||
| } | ||
| blaze_config['overwrite'] <- NULL | ||
| for (arg in names(blaze_config)) { | ||
| blaze_argv <- paste(blaze_argv, paste0('--',arg), blaze_config[arg])} | ||
|
|
||
| # prepare 10X whitelist | ||
| temp_path <- tempfile() | ||
| bfc <- BiocFileCache::BiocFileCache(temp_path, ask = FALSE) | ||
| bc_list_10x_url <- 'https://github.com/shimlab/BLAZE/raw/main/10X_bc/3M-february-2018.zip' | ||
| cat('Downloading the full whitelist from 10X...') | ||
| bc_list_10x <- bfc[[names(BiocFileCache::bfcadd(bfc, 'bc_list_10x', bc_list_10x_url))]] | ||
| blaze_argv <- paste(blaze_argv, '--full-bc-whitelist', bc_list_10x) | ||
|
|
||
| blaze_argv <- paste(blaze_argv, fq_in) | ||
|
|
||
| ret <- | ||
| callBasilisk(flames_env, function(blaze_argv) { | ||
|
|
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| blaze_path <- system.file("blaze", package = "FLAMES") | ||
| cat("Running BLAZE...\n") | ||
| cat("Argument: ", blaze_argv, "\n") | ||
| blaze <- | ||
| reticulate::import_from_path("blaze", blaze_path) | ||
| ret <- | ||
| blaze$main(blaze_argv) | ||
|
|
||
| ret | ||
| }, blaze_argv = blaze_argv | ||
| ) | ||
| #ret # return the filename of demultiplexed fastq | ||
| } |
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| @@ -0,0 +1,4 @@ | ||
| #' FLAMES: full-length analysis of mutations and splicing | ||
| #' @name FLAMES | ||
| #' @useDynLib FLAMES, .registration=TRUE | ||
| NULL |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,66 +1,31 @@ | ||
| # flames_nopysam_env <- BasiliskEnvironment( | ||
| # envname = "flames_nopysam_env", pkgname = "FLAMES", | ||
| # packages = c( | ||
| # "python==2.7.15.0", | ||
| # # "minimap2==2.17", | ||
| # "numpy==1.16.5", | ||
| # "editdistance==0.5.3", | ||
| # "bamnostic==1.1.7" | ||
| # ), | ||
| # channels = c("bioconda", "conda-forge") | ||
| # ) | ||
|
|
||
| #' @importFrom basilisk BasiliskEnvironment | ||
| flames_env <- BasiliskEnvironment( | ||
| envname = "flames_env", pkgname = "FLAMES", | ||
| pip = c("fast-edit-distance==1.2.0"), | ||
| packages = c( | ||
| "python==3.7", | ||
| # "minimap2==2.17", | ||
| "numpy==1.16.5", | ||
| "editdistance==0.5.3", | ||
| "scipy==1.2.0", | ||
| "pysam==0.18.0" | ||
| "python==3.10", | ||
| "numpy==1.25.0", | ||
| "editdistance==0.6.2", | ||
| "scipy==1.11.1", | ||
| "pysam==0.21.0", | ||
| "cutadapt==4.4", | ||
| "tqdm==4.64.1", | ||
| "matplotlib==3.5.3", | ||
| "pandas==1.3.5", | ||
| "biopython==1.79" | ||
| ), | ||
| channels = c("bioconda", "conda-forge") | ||
| channels = c("conda-forge", "bioconda", "defaults") | ||
| ) | ||
| # flames_env <- BasiliskEnvironment(envname="full_env", | ||
| # pkgname="FLAMES", | ||
| # packages=c("python==2.7.15.0", | ||
| # "pysam==0.16.0.1", | ||
| # "minimap2==2.17", | ||
| # "numpy==1.16.5", | ||
| # "editdistance==0.5.3", | ||
| # "bzip2==1.0.8", | ||
| # "c-ares==1.11.0", | ||
| # "ca-certificates==2020.11.8", | ||
| # "certifi==2019.11.28", | ||
| # "htslib==1.11", | ||
| # "k8==0.2.5", | ||
| # "krb5==1.17.1", | ||
| # "libblas==3.9.0", | ||
| # "libcblas==3.9.0", | ||
| # "libcurl==7.71.1", | ||
| # "libcxx==11.0.0", | ||
| # "libdeflate==1.6", | ||
| # "libedit==3.1.20191231", | ||
| # "libev==4.33", | ||
| # "libffi==3.2.1", | ||
| # "libgfortran==3.0.0", | ||
| # "libgfortran5==9.3.0", | ||
| # "liblapack==3.9.0", | ||
| # "libnghttp2==1.41.0", | ||
| # "libopenblas==0.3.12", | ||
| # "libssh2==1.9.0", | ||
| # "llvm-openmp==11.0.0", | ||
| # "ncurses==6.2", | ||
| # "openssl==1.1", | ||
| # #"pip==20.1.1", | ||
| # "python_abi==2.7", | ||
| # "readline==8.0", | ||
| # "setuptools==44.0.0", | ||
| # "sqlite==3.33.0", | ||
| # "tk==8.6.10", | ||
| # "wheel==0.35.1", | ||
| # "xz==5.2.5", | ||
| # "zlib==1.2.11"), | ||
| # channels=c("bioconda", "conda-forge")) | ||
|
|
||
| # blaze_env <- BasiliskEnvironment( | ||
| # envname = "blaze_env", pkgname = "FLAMES", | ||
| # pip = c("fast-edit-distance==1.2.0"), | ||
| # channels = c('conda-forge','bioconda', 'defaults'), | ||
| # packages = c( | ||
| # "python==3.7", | ||
| # "biopython==1.79", #blaze specific | ||
| # "pandas==1.3.5",#blaze specific | ||
| # "numpy==1.21.6", #blaze specific | ||
| # "matplotlib==3.5.3", #blaze specific | ||
| # "tqdm==4.64.1" | ||
| # )) |
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