Question: Bash and seqret problem
0
gravatar for MichaelTrev
11 months ago by
MichaelTrev10
MichaelTrev10 wrote:

Hi! This time I have a problem with bash. I'm working on Linux, but bash is unfamiliar to me. I need to change format clustal to fasta. Someone help me in another post, and I know I can do that with seqret.

So now: i have in directory 40 files with ".aln" end. I can manually by terminal type

seqret <file.aln> <output.fasta>

But I need to do that automatically. Can someone tell me how to do it so that all files in dir are changed with one script? I'm asking for help coz I need results quickly, and I can not deal with this issue (i will learn bash asap). I need result in separate files. Thanks in advance!

bash script seqret • 366 views
ADD COMMENTlink written 11 months ago by MichaelTrev10

You can try to put it in a for loop.

ADD REPLYlink written 11 months ago by Benn7.9k
2
gravatar for Joe
11 months ago by
Joe16k
United Kingdom
Joe16k wrote:

Or use parallel:

ls *.aln | parallel "seqret {} {.}.fasta"
ADD COMMENTlink written 11 months ago by Joe16k

I'ts working, awesome! Thank U for help. I should definitely read about it ;)

ADD REPLYlink written 11 months ago by MichaelTrev10
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