Experiencing trouble with rf-rctools merge

[Asperatus22]

Hi, Thanks for the works. While trying to merge two rc file with rf-rctools merge :

rf-rctools merge \ -o rf_count_merge_NM/NM_merge.rc -ow \ -i ./rf_count_fusion_impair_NM/index.rci,./rf_count_fusion_pair_NM/index.rci \ # tryed with ./ and without rf_count_fusion_impair_NM/19-190123.rc rf_count_fusion_pair_NM/20-190123.rc

i have this error : [!] Error: Provided RCI index file "rf_count_fusion_impair_DMS/index.rci,rf_count_fusion_pair_DMS/index.rci" does not exist

Maybe an argument parsing error ?

while i try to run the code with only one argument for the index : rf-rctools merge \ -o rf_count_merge_NM/NM_merge.rc -ow \ -i ./rf_count_fusion_impair_NM/index.rci \ # tryed with ./ and without rf_count_fusion_impair_NM/19-190123.rc rf_count_fusion_pair_NM/20-190123.rc

i run into this error : [!] Exception [RF::Data::IO::RC->new()]: No such file or directory -> Caught at /nfs/bin/RNAFramework/lib/Core/Base.pm line 126.

any kind of help would be appréciate. Best regards Lionel

[dincarnato]

Hi Lionel,

hard for me to understand what is going on. I have a hunch: does the rf_count_merge_NM folder exist? Cause rf-rctools merge won't generate it in case it doesn't.

Can you please send over the files so that I can try? You can send them to my email: dincarnato@rnaframework.com

Best, Danny

[Asperatus22]

the rf_count_merge_NM folder didn't exist.

I added a "check and create folder" in my code and the code run well, but only with a unique .rci file. This could be a code improvement or a documentation warning.

I still encounter the first error with multiple .rci Do you still need my file to test with ?

Thank you for your help and reactivity.

[dincarnato]

Ohhh, now I see the issue! Yes, please try to git pull and let me know if this solves.

Best, Danny

[Asperatus22]

Yess, it works well. Thanks a lot Lionel