Separate lines based on some character?

Question

[star]

I have a fasta file like below, I like to seprate only coordinate and add one column with "hello" name.

>Human|chr16:80372593-80373755 | element 4 | positive  | neural tube[6/10] | hindbrain (rhombencephalon)[10/10] | midbrain (mesencephalon)[10/10]
gtgaCAGAGACAGACAGTGACAGAGACAgattttagaatttgaacaaaggtaaataagag

>Human|chr16:78510608-78511944 | element 12 | positive  | hindbrain (rhombencephalon)[9/11] | forebrain[9/11]
AAGCTAGCTAATTGCTTCTTCAGTTGaagacctaaatgagttttaaagtgaaatgcatat

Expect file:

chr16:80372593-80373755         hello
chr16:78510608-78511944         hello

[lieven.sterck]

what do you consider 'name' (== which of the fields in your fasta header?)

[star]

I like to add my favorite name.

[GenoMax]

Will change for each entry or stay the same?

[star]

it is the same name.

Answer 1

[Pierre Lindenbaum]

awk -F '|' '/^>/ { print $2 "\thello"}' jeter.fa

[Bastien Hervé]

If you get annoyed by the extra space after chr16:80372593-80373755 :

awk -F '|' '/^>/ { print substr($2, 1, length($2)-1) "\thello"}' jeter.fa

[Pierre Lindenbaum]

I would just use -F '[| ]' ...

[Bastien Hervé]

Yes it is quicker, but if they got a space in the id name the command fails