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Thank you, that works beautifully :)

I have been using grep to output whole lines using a pattern file with identifiers (fileA):

fig|562.2322.peg.1
fig|562.2322.peg.3
fig|562.2322.peg.3
fig|562.2322.peg.3
fig|562.2322.peg.7
From...

For anyone that might be facing similar problems, I ended up with this solution:


for k in Anno_**
do
Var1=$(find $k -name "Anno*" | grep -o '[0-9]\{3,\}[.][0-9]\{4,\}')
for l in Scan**
do...

I tested the suggestions of SriniShoo, but this seems to output the numerical patterns of all filenames, while I need to recursively read the pattern from each filename into the variable (in a for...

I am writing a bash script where I use two types of files that both contain a numerical pattern of the type 123.4567 (always groups of three and four digits separated by period) within their...

Is it also possible to modify this code, for example using a for-loop, to perform this action on all .fasta files in a directory (outputing the modified files to a new directory or similarly)?

Brilliant, thank you! :b:

I did, but it was removed.. here goes again: fasta files (e.g. sample_1.fasta) in format:

>node_1
atgatgatgat
>node_3
gtcgtcgtcgtcgtc
>node_12
gtagtagta

Expected output:
...

Gave awk a try, but this appears to print the filename in the first header only, not to change it in place, and also this does not affect the subsequent headers. Any alternative solutions?

How do we append the file name to fasta file headers in multiple fasta-files in Linux?