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I've got done the following parameter shell expansion:

trihead="$(cat ../FASTA_SEC/"$i".fa)"
echo "${trihead#"${trihead%%[!A]*}"}" > ../FASTA_SEC/"$i".fa

I'd like to trim the leading A's from the second line of a fasta file (a kind of plain text format .fa)

the input would be something like:

>B4-0K032_18670_015
AAAAAAANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCNNNGNNNTAGATACAAGCGAGCGGC

and i'd like the output to be like:

>B4-0K032_18670_015
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCNNNGNNNTAGATACAAGCGAGCGGC

By the way, does anybody know some side where shell parameter expansion is well explained?

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  • 2
    Please edit your question and explain i) what the command is supposed to be doing and ii) what it is actually doing. Also, this isn't a bioinformatics site, people here have no idea what FASTA is. Please include an example of your input file and show us the output you would like to see. – terdon♦ Jan 13 '17 at 17:19
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    Don't read a fasta file into a variable. It looks more like this is a job for sed or awk, depending on what it is you're trying to achieve on that second line. – Kusalananda♦ Jan 13 '17 at 17:23
  • Edited sorry! I though about sed sth like sed -e '4 {all leading A's}' > file but iunno how to order sed to delete leading A's from 2nd line not all A's or so.. – Neuls Jan 13 '17 at 17:33
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To trim the leading consecutive As out of the second line of a file (and then replace the original file with the result):

$ sed '2s/^A*//' data.fa >data.out  &&  mv data.out data.fa

The sed command applies the substitution command (s) to line 2 specifically in this example. It will substitute any number of As at the start of the line with nothing.

The pattern is ^A* which means "match zero or more (*) of the single character A at the start of the line (^)".

The reason I don't use sed -i (for "in-place editing") is that the -i flag is horribly non-portable between sed implementations.

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  • so to order A leading characters do u use ^ ? for trimming tailing A's you do sed '/^N*//g' file – Neuls Jan 13 '17 at 17:44
  • ^ is the regular expression anchor for "Start of the line". – DopeGhoti Jan 13 '17 at 17:45
  • @Neuls The ^ is called an "anchor". It anchors the pattern (A*) to the start of the line. The anchor for the end or the line is $. – Kusalananda♦ Jan 13 '17 at 17:45
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This will remove all leading As from a line following a line that start with >:

sed '/^>/n;s/^A*//' /path/to/file

If the output is what you want, and you want to edit the original file, use:

sed --in-place '/^>/n;s/^A*//' /path/to/file
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