alingment ID in STOCKHOLMs output

[darked89]

Hello,

I used mlocarna to align tRNA isoforms. All works fine as far as I can tell, but the STOCKHOLM format files do not contain identifiers (which is to be expected).

I am getting:

# STOCKHOLM 1.0
#=GF CC Generated by LocARNA 2.0.0
#=GF SQ 26

tRNA-Ala-AGC-6-1   GGGGGUAUAGCUCA<snip>

what I need is:

# STOCKHOLM 1.0
#=GF ID tRNA-Ala-AGC

tRNA-Ala-AGC-1-1    GGGGGUATAGCUCAGU<snip>

Would you consider adding an extra feature/command line switch, i.e.:

 mlocarna --stockholm --threads 6 --name tRNA-Ala-AGC  tRNA-Ala-AGC.fa

Many thanks for your help

Darek Kedra

[s-will]

Thanks for your suggestion. I see that it can be desirable to automatically include id or other meta data in the generated stk files. Spontaneously, I imagine, a good way to achieve that in more generality could be to support copying meta-data from input stk files in future releases. It could also make sense to include the input filename as GF ID (or GF AC !?). Generally, including such features in LocARNA is always prone to end up in over-specialized solutions, therefore I would suggest another solution (at least in the meantime), namely post-process the output of LocARNA:

A simple scriptable way to add the ID tag to a LocARNA-generated stk file could use sed:
sed -i '3i #=GF ID tRNA-Ala-AGC' result.stk

Let me know what you think about such solutions; discussion is always appreciated.

[darked89]

Dear Sebastian,

Thank you for your sed oneliner.
I ended up writing a small Python script going through all result.stk files and putting the corresponding ID lines. So in that way the issue is resolved.
I will provide the link to the script after some cleanup.

Warm greetings,

DK