umccr/RNAsum

Replace Carriage Return (`^M`) in reference `Target.txt` files

pdiakumis opened this issue · 1 comments

pdiakumis commented

The *Target.txt files seem to have been generated on a Windows system and appear as single-line files on GitHub and unix systems. This causes issues with downstream parsing, where some R functions ignore the final data 'line' (and others work probably out of pure luck). Need to use something like dos2unix on those. Maybe one for when we reorg/update the data.
Example: https://github.com/umccr/RNAsum/blob/6cb7d0e12291c6e356cd292cf5ac0b4cb15d3a98/data/ref_data/TCGA_ACC_Target.txt

$ wc -l TCGA_ACC_Target.txt
       1 TCGA_ACC_Target.txt

$ cat -ve TCGA_ACC_Target.txt
Sample_name	Target^MTCGA-OR-A5J1-01A-11R-A29S-07	ACC (TCGA)^MTCGA-OR-A5J2-01A-11R-A29S-07	ACC (TCGA)^MTCGA-OR-A5J3-01A-11R-A29S-07	ACC (TCGA)^MTCGA-OR-A5J5-01A-11R-A29S-07	ACC (TCGA)^MTCGA-OR-A5J6-01A-31R-A29S-07	ACC (TCGA)^MTCGA-OR-A5J7-01A-11R-A29S-07