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Speedup FRASER couting on Cluster #266

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Speedup FRASER couting on Cluster #266

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6185ffc
copy BAM file to local disk
mumichae Oct 20, 2021
fdb49d9
Merge branch 'dev' into local_fraser
mumichae Nov 17, 2021
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13 changes: 13 additions & 0 deletions drop/modules/aberrant-splicing-pipeline/Counting/01_1_countRNA_splitReads_samplewise.R
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,15 @@ if(strandSpecific(fds) == 0){
genome <- getBSgenome(genomeAssembly)
}

# Copy to local tmp
bamFile <- bamFile(fds[, samples(fds) == sample_id])[[1]]
tmp_file <- file.path(snakemake@resources$tmpdir, paste0('split_counts_', sample_id, '.bam'))

message('Copy ', bamFile, ' to ', tmp_file)
file.copy(bamFile, tmp_file)
file.copy(paste0(bamFile, '.bai'), paste0(tmp_file, '.bai'))
bamFile(fds[, samples(fds) == sample_id]) <- tmp_file

# Count splitReads for a given sample id
sample_result <- countSplitReads(sampleID = sample_id,
fds = fds,
Expand All @@ -50,4 +59,8 @@ sample_result <- countSplitReads(sampleID = sample_id,
message(date(), ": ", dataset, ", ", sample_id,
" no. splice junctions (split counts) = ", length(sample_result))

# Reset bam file
bamFile(fds[, samples(fds) == sample_id]) <- bamFile
file.remove(tmp_file)

file.create(snakemake@output$done_sample_splitCounts)
13 changes: 13 additions & 0 deletions drop/modules/aberrant-splicing-pipeline/Counting/01_3_countRNA_nonSplitReads_samplewise.R
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Expand Up @@ -35,6 +35,15 @@ sample_id <- snakemake@wildcards[["sample_id"]]
# Read splice site coordinates from RDS
spliceSiteCoords <- readRDS(snakemake@input$spliceSites)

# Copy to local tmp
bamFile <- bamFile(fds[, samples(fds) == sample_id])[[1]]
tmp_file <- file.path(snakemake@resources$tmpdir, paste0('nonsplit_counts_', sample_id, '.bam'))

message('Copy ', bamFile, ' to ', tmp_file)
file.copy(bamFile, tmp_file)
file.copy(paste0(bamFile, '.bai'), paste0(tmp_file, '.bai'))
bamFile(fds[, samples(fds) == sample_id]) <- tmp_file

# Count nonSplitReads for given sample id
sample_result <- countNonSplicedReads(sample_id,
splitCountRanges = NULL,
Expand All @@ -48,4 +57,8 @@ sample_result <- countNonSplicedReads(sample_id,
message(date(), ": ", dataset, ", ", sample_id,
" no. splice junctions (non split counts) = ", length(sample_result))

# Reset bam file
bamFile(fds[, samples(fds) == sample_id]) <- bamFile
file.remove(tmp_file)

file.create(snakemake@output$done_sample_nonSplitCounts)