I have say 100 text files of which 50 of them have file name starting with sshv2l and other fifty without sshv2l. I want to merge them in a loop like this (below) where I have two sets of merged files. For the ones with sshv2l, I did something like below, but could not merge files without sshv2l. How do I write if not condition within for loop in bash?
for f in sshv2l*; do
echo "Merging file :" $f
cat ${f} >> sshv2l_merged.fastq
done
Your loop code can just be replaced with single cat:
cat sshv2l* >> /path/to/sshv2l_merged.fastq
Now to grab all the files not starting with sshv2l you can use extglob negation glob:
# enable extglob
shopt -s extglob nullglob
cat !(sshv2l*) >> /path/to/not_sshv2l_merged.fastq
# disable extglob
shopt -u extglob nullglob
I have added some imaginary /path/to/ path to make sure you keep *.fastq files outside current directory to avoid them getting concatenated in cat commands.
exec bash then source ~/.bashrc.