I found this little code which I put in a .bash_profile file
lenFunc() {
echo ${#1}
}
alias len=lenFunc
Typing actg in terminal outputs 4.
I then learned that echo actg|rev outputs gtca. However, I have troubles creating an alias from it.
Neither of these two works for me:
alias revFunc() {
echo ${#1}|rev
}
alias rev=renFunc
and
alias rev='echo "$1"|rev'
Help is appreciated!
(bonus: if anyone knows a way I can upgrade and also have a "revcom" command for reverse complementary I'll give you a virtual hug)
I run macOS if it matters.
2 answers
Why did you put an alias before the function declaration?
It should be
revFunc() {
echo ${1} | rev
}
## => also removed the # inside {1} as yu want to print rather than count the input.
alias REV=revFunc
## gives:
REV 1234
> 4321
Also, avoid alias names that are identical to existing system commands like rev, use REV, myrev or similar instead.
There was also a typo: alias rev=renFunc was re=>N<=Func instead of re=>V<=Func
For reverse complements, see e.g. fasta - reverse complement sequence or a super-simple https://bioinformatics.stackexchange.com/questions/7458/what-is-a-quick-way-to-find-the-reverse-complement-in-bash which would then be
revComp() {
echo $1 | tr ACGTacgt TGCAtgca | rev
}
revComp AAAACCTG
>CAGGTTTT
You just need to remove the alias in your function and change the first argument to $1 as you are not interested in the length i.e. $#1
revFunc() {
echo ${1}|rev
}
For reverse compliment you can change the function to be
revComp() {
echo ${1}|tr "[ATGCatgc]" "[TACGtacg]"|rev
}
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