Closed dsampath31 closed 5 months ago
If I use the unfiltered pigeon classification file, edited the Rscript number of arguments and applied sed "s/within_cage_peak/within_CAGE_peak/g
then the script ran fine producing PDF and HTML.
I am wondering why applying the *lite_classification.txt still fails with the error above. Also, the main script requires change in the number of arguments and reflect the latest release with uppercase "CAGE"
Please report to the appropriate repository. We don't maintain SQANTI3
Operating system MAC
Package name https://github.com/ConesaLab/SQANTI3/blob/master/utilities/report_pigeon/pigeon_report.R Rscript used to provide reports from pigeon, (pigeon 1.1.0)
Conda environment Using Mac's Rstudio server
Describe the bug There is a bug in line 15 in pigeon_report.R script as the number of arguments is 5 not 6. class.file <- args[1] junc.file <- args[2] utilities.path <- args[4] saturation.curves <- args[5] report.format <- args[6]
if (length(args) < 6) { stop("Incorrect number of arguments! Script usage is: [classification file] [junction file] [utilities directory path] [True/False for saturation curves] [pdf|html|both]. Abort!") }
Error message I correct the arguments number and run the script
Rscript ~/Documents/isoseq/SQANTI3/utilities/report_pigeon/pigeon_report.R *lite_classification.txt *lite_junctions.txt ~/Documents/isoseq/SQANTI3/utilities/report_pigeon/ False both