sed to replace pattern with filename

Shell Programming and Scripting
1

Hi all,

I'm trying to replace a pattern/string in about 100 files with the filename using following commands but getting nowhere:

for f in .fa; do sed "s/^>./>$f/g" $f > $f_v1.fa; done

for f in .fa; do sed 's/^>./>`echo $f`/' > $fa_v1.fa; done

Basically I want to change any line that starts with > to >filename.

Thanks for any suggestion.

2 
 
for f in *.fa; do sed 's/^>.*/>'$f'/' $f > ${f}_v1.fa; done
3

This solves my problem. Thank you.

By the way can you explain the single quotation '$f'? I have tried with double quotation and it simply replaced the line with "$f". And why the curvy bracket at the end? Apology if the answers are very obvious. I'm actually a biologist. Thank you.

4

To single quotes gets the shell variable $f as part of the sed script between the first and last quote.

5

Curvy bracket is used to distinguish the actual variable name. Without curvy bracket is will consider the whole as variable name: $f_v1.fa; but with curvy bracket it will consider only $f as variable name: ${f}_v1.fa;

6

To be precise, without the braces, the variable name ends with the character before the dot, ${f_v1}.fa , since the dot is not allowed in a variable name [1].

Regards,
Alister

  1. ksh does allow dots in a variable name, but those names MUST appear within braces
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