Remove two substrings from a string

Question

I have a list of files like this:

wgEncodeCaltechRnaSeqGm12878R1x75dFastqRep1.fastq.trim.tags.sam
wgEncodeCaltechRnaSeqGm12878R1x75dFastqRep2.fastq.trim.tags.sam
wgEncodeCshlLongRnaSeqGm12878CellPapFastqRd1Rep1.fastq.trim00.tags.sam
wgEncodeCshlLongRnaSeqGm12878CellPapFastqRd1Rep1.fastq.trim01.tags.sam
wgEncodeCshlLongRnaSeqGm12878CellPapFastqRd1Rep1.fastq.trim02.tags.sam
wgEncodeCshlLongRnaSeqGm12878CellPapFastqRd1Rep2.fastq.trim00.tags.sam
wgEncodeCshlLongRnaSeqGm12878CellPapFastqRd1Rep2.fastq.trim01.tags.sam
wgEncodeCshlLongRnaSeqGm12878CellPapFastqRd1Rep2.fastq.trim02.tags.sam
wgEncodeCshlLongRnaSeqGm12878CellPapFastqRd2Rep1.fastq.trim00.tags.sam
wgEncodeCshlLongRnaSeqGm12878CellPapFastqRd2Rep1.fastq.trim01.tags.sam

I want to remove the Rd1, Rd2 and .sam stings from their file names. With the following bash script, I can remove the Rd1, Rd2 and .sam strings using two commands....

for i in $(ls)

do

echo "${i/Rd?/}"
echo "${i/.sam/}"

done

But I want to know how to do the two substitutions in one step Do you know how to do it?

Thanks for your time!

Answer 1

You can use extended patterns to do it all in bash.

shopt -s extglob
echo ${i//@(Rd?|.sam)}

Here's the breakdown:

1. Use // to replace all occurrences of the pattern, not just the first.
2. @(Rd?|.sam) is an extended pattern, which matches either Rd? or .sam. The pipe separates the two sub-patterns.

Technically, you'd like to be able to avoid removing ".sam" from the middle of the word, but it looks like this is safe for your use case.

Answer 2

Of course we know!

for i in *
do
   echo $i | sed 's/Rd.//;s/\.sam$//'
done

And when you want rename these files:

for i in *
do
   mv "$i" "$(echo $i | sed 's/Rd.//;s/\.sam$//')"
done