key values list in R for command line arguments-CodePudding

Rscript test.R ../Data/bam/a.bam:0 ../Data/bam/b.bam:0.1 ../Data/bam/c.bam:0.5 ../Data/bam/d.bam:1

I want to make a list of keys and values for commandline arguments. I have use following code.

#test.R
args <- commandArgs(trailingOnly = TRUE)

key_value_pairs <- strsplit(args, " ")
key_value_pairs <- lapply(key_value_pairs, function(x) strsplit(basename(x), ":")[[1]])
key_value_pairs <- as.data.frame(key_value_pairs, stringsAsFactors = FALSE)

colnames(key_value_pairs) <- c("key", "value")
key_value_pairs$value <- as.numeric(key_value_pairs$value)

print(key_value_pairs)

i got follwoing output:

 key value
1 a.bam    NA
2                                           0  
                                           NA
1 b.bam
2                                        0.1
                                           NA
1 c.bam
2                                         0.5
                                           NA
1 d.bam
2                                        1
                                           NA

but i want out like:

key value
a.bam  0.0
b.bam  0.1
c.bam  0.5
d.bam  1

Can someone help me to find the issue and how to solve it. Thanks

#test.R
args <- commandArgs(trailingOnly = TRUE)

key_value_pairs <- strsplit(args, " ")
key_value_pairs <- lapply(key_value_pairs, function(x) strsplit(basename(x), ":")[[1]])
key_value_pairs <- as.data.frame(key_value_pairs, stringsAsFactors = FALSE)

colnames(key_value_pairs) <- c("key", "value")
key_value_pairs$value <- as.numeric(key_value_pairs$value)

print(key_value_pairs)

CodePudding user response：

Note that the command args are already separated by space so you don't need to do that yourself. And you need a different strategy for creating your data.frame. This should work

args <- commandArgs(trailingOnly = TRUE)
key_value_pairs <- lapply(args, function(x) strsplit(basename(x), ":")[[1]])
key_value_pairs <- as.data.frame(do.call("rbind", key_value_pairs), stringsAsFactors = FALSE)

colnames(key_value_pairs) <- c("key", "value")
key_value_pairs$value <- as.numeric(key_value_pairs$value)
key_value_pairs
#     key value
# 1 a.bam   0.0
# 2 b.bam   0.1
# 3 c.bam   0.5
# 4 d.bam   1.0

An alternate way to do this would be

args <- commandArgs(trailingOnly = TRUE)
key_value_pairs <- read.table(text=basename(args), sep=":",
    col.names = c("key", "value"))

That will pretty much do everything in one go.