3.2 years ago by
This is not really a Galaxy question .. but I can't help but share a simple and super useful line-command option that will work here.
- Make a clone-copy of the file you intend to modify (the one with the "compNNNNN_c0_seq1" content). Put the backup file in another place completely - like a directory labeled as "YYYYMMDD_originals_experiment-name" or something else obvious. (sub-directories tend to not be the best place for backups IMHO .. too easy to "rm -rf" and lose it all)
With the working copy of the file - let's call it "contigs.fasta" - execute the following at the prompt ($ == prompt):
$ sed 's/_seq1//' configs.fasta > configs_clean.fasta
There are literally at least 30 ways to do this sort of manipulation, sed is just my favorite line-command. Short and sweet.
The identifiers could also be modified to add-on the "_seq" bit. I personally would use "vi" or whatever your favorite text editor is for that.
- Backup! and call the file something like "identifiers.txt"
- Assumption: file is a single column list of identifiers, only!
$ vi identifiers.txt
within vi, while escaped (hit "esc" key if needed), type:
:%s/$/_seq1/ (hit return)
Either can be done within Galaxy itself using text manipulation tools. More about these commands & options can be googled.
Best, Jen, Galaxy team