Amplified_Prediction_script copy.Rmd

pylelab / MRTModSeq

Modification profiling with Marathon RT

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Amplified_Prediction_script copy.Rmd #1

Closed kad-ecoli closed 2 years ago

kad-ecoli commented 2 years ago

A few suggestions on the code:

Please remove unnecessary library inclusion. For example, library(readxl) is unnecessary given that excel input are no longer used. In fact, you only use dplyr and foreign.
Line 25 Amplified-TRNA-Huh-5_8S_Untreated_5_8_mutation_counts.txtt should probably be changed to Amplified-TRNA-Huh-5_8S_Untreated_5_8_mutation_counts.txt
Please try to avoid space in the file name and folder name, as spaces create unnecessary difficulties for typing in the command line.
The line @attribute Modifications should be automatically written rather than manually changed by the user.

kad-ecoli commented 2 years ago

ratesfun <- function(x,y) {
  x / y
}

Should we consider case where y==0?

kad-ecoli commented 2 years ago

Amplified_Prediction_script.R.zip Please see an example where the command line argument is used to specified the input file name. To run the program:

mkdir test
cd test

Rscript  ../Amplified_Prediction_script.R "../sample 5.8S rRNA data input and output/amplified_predictions_script INPUTS/Amplified-TRNA-Huh-5_8S_5_8_profile.txt" "../sample 5.8S rRNA data input and output/amplified_predictions_script INPUTS/Amplified-TRNA-Huh-5_8S_Untreated_5_8_mutation_counts.txt" "../sample 5.8S rRNA data input and output/amplified_predictions_script INPUTS/Amplified-TRNA-Huh-5_8S_Modified_5_8_mutation_counts.txt"

Here, only the input file names are specified by command line arguments, while output file names are hard coded, which should not be a big problem so long as the output is in the current folder.

pylelab commented 2 years ago

Thank you so much Chengxin! Huge help. Have made some small changes, and have also added the output_reordering.r file.