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loopsbioinformaticsrscriptape-phylo

How to use a variable to specify an output file name in R?

I'm trying to write an Rscript to run the phylogenetics package ape to run the same command on many input files and produce an output file for each one with a modified version of the original file name.

Here is the code I'm trying to use:

library(ape)
setwd("/home/wirenia/phylogenomics_projects/Monoplacophora    /2014-09-10_Monoplacophora_fixed_alicut/pruned/OGs_with_LANT/manually_cleaned_alignments/2019-06-19_IQ-TREE_single-gene_trees/")
for (x in list.files(pattern="*.treefile")) {
tree <- read.tree(x)
tree$node.label <- NULL
write.tree(tree, file = x'.nobootstraps.tre')
}

The issue is clearly on the write.tree line, but I can't figure out how to fix it. Here's the error message I'm getting:

Rscript remove_bootstrap_support_values_from_newick_trees.r
Error: unexpected string constant in:
"tree$node.label <- NULL
write.tree(tree, file = tree'.nobootstraps.tre'"
Execution halted

Any assistance would be greatly appreciated.

Thanks!

Solution

  • I believe you need :

    write.tree(tree, file = paste(x, '.nobootstraps.tre'))

    instead of your

    write.tree(tree, file = x'.nobootstraps.tre'

    R cannot concatenate strings like you try stringvariable"stringliteral"

    If you have more bioinformatics related questions in the future I suggest moving to https://bioinformatics.stackexchange.com/, I think you will get much quicker replies there.