Critical bug in compareBed.sh

[renewiegandt]

I'm running following code:

./compareBed.sh -d /mnt/agnerds/masterjlu2018/out6/footprint_extraction/mDuxPos_footprints_called_peaks.bed -m /mnt/workspace1/rene.wiegandt/tmp7/ --fasta /mnt/agnerds/masterjlu2018/testdata/presentation/mm10_chr.fa -o test.bed -p /mnt/agnerds/Rene.Wiegandt/10_Master/masterJLU2018/bin/1.2_filter_motifs/

It exsits with following error:

Warning message:
In fread(paste(folder, "/pass2Tr.bed", sep = "")) :
  File '/mnt/agnerds/Rene.Wiegandt/10_Master/masterJLU2018/bin/1.2_filter_motifs//pass2Tr.bed' has size 0. Returning a NULL data.table.
Error in setnames(x, value) :
  Can't assign 8 names to a 0 column data.table
Calls: colnames<- -> names<- -> names<-.data.table -> setnames
Execution halted
Error: The requested file (/mnt/agnerds/Rene.Wiegandt/10_Master/masterJLU2018/bin/1.2_filter_motifs//merged.bed) could not be opened. Error message: (No such file or directory). Exiting!

• 1. Your script should check if the given path has a '/' at the end and consider this when building a path!
• 2. The merged.bed file is not written to the location where your script expects it to be. Could be because of 1. but it could also be something else. Please look into that.
• 3. You should add a description for parameter -p; --path

[renewiegandt]

I get the same error is if the paths do not contain '//'. Something is wrong with the script when the parameter -p is set.

[HendrikSchultheis]

In the warning above you use paste to construct a file path. Please use file.path instead as it is platform independent and faster.

[HendrikSchultheis]

@JannikHamp is this all addressed in #33?

[renewiegandt]

It is!