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FLASSO_RSCRIPT = """\
#!/usr/bin/env Rscript
# Calculate copy number segmentation by Fused Lasso.
# Input: log2 coverage data in CNVkit's tabular format
# Output: the CBS-style SEG data table
library('cghFLasso')
tbl <- read.delim("%(probes_fname)s")
write(paste("Segmenting", levels(tbl$chromosome)), stderr())
fit <- cghFLasso(tbl$log2, FDR=%(threshold)g, chromosome=tbl$chromosome)
# Reformat the output table as SEG
outtable <- data.frame(sample="%(sample_id)s",
chromosome=tbl$chromosome,
start=tbl$start,
end=tbl$end,
nprobes=1,
value=fit$Esti.CopyN)
write("Printing the segment table to standard output", stderr())
write.table(outtable, '', sep='\t', row.names=FALSE)
"""
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