How to place "\n" after each sequence in a fasta file?

Question

[AsoInfo]

Hi, I would like to place "\n" after every sequence in a FASTA file. My FASTA file looks like this:

>pdb|5U15|L Chain L, Crystal Structure Of Dh270.uca3 (unliganded) From The Dh270 Broadly Neutralizing N332-glycan Dependent Lineage
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEVSKRPSGVSNRFSGSKSG
NTASLTISGLQAEDEADYYCCSYAGSSTVIFGGGTKLTVLGQPKGAPSVTLFPPSSEELQANKATLVCLI
SDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTV
APTECS
>pdb|5U15|H Chain H, Crystal Structure Of Dh270.uca3 (unliganded) From The Dh270 Broadly Neutralizing N332-glycan Dependent Lineage
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTM
TRDTSISTAYMELSRLRSDDTAVYYCARGGWISLYYDSSGYPNFDYWGQGTLVTVSGASTKGPSVFPLAP
SSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC
NVNHKPSNTKVDKRVEPKSCDKHHHHHH

I would like to modify the file as:

>pdb|5U15|L Chain L, Crystal Structure Of Dh270.uca3 (unliganded) From The Dh270 Broadly Neutralizing N332-glycan Dependent Lineage
QSALTQPASVSGSPGQSITISCTGTSSDVGSYNLVSWYQQHPGKAPKLMIYEVSKRPSGVSNRFSGSKSG
NTASLTISGLQAEDEADYYCCSYAGSSTVIFGGGTKLTVLGQPKGAPSVTLFPPSSEELQANKATLVCLI
SDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTV
APTECS

>pdb|5U15|H Chain H, Crystal Structure Of Dh270.uca3 (unliganded) From The Dh270 Broadly Neutralizing N332-glycan Dependent Lineage
QVQLVQSGAEVKKPGASVKVSCKASGYTFTGYYMHWVRQAPGQGLEWMGWINPNSGGTNYAQKFQGRVTM
TRDTSISTAYMELSRLRSDDTAVYYCARGGWISLYYDSSGYPNFDYWGQGTLVTVSGASTKGPSVFPLAP
SSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYIC
NVNHKPSNTKVDKRVEPKSCDKHHHHHH

I have encountered a post regarding linearizing the fasta file but couldnt figure it out.

[GenoMax]

Title of this post does not appear to match the request in the main body of the post. If you just want to add a gi_ before pdb you could use sed 's/^>pdb/\>gi\_pdb/g' your_file > new_file.

[AsoInfo]

I have just edited the post. "gi" was added mistakingly.

Answer 1

[Joe]

A very simple solution would be:

cat file.fasta | sed 's/>/\n>/g' | tail -n+2

It'll add an empty line at the start of the file as well though, but I don't know if thats a problem for you. Linearising the fasta and appending to the end of the sequence line would be a more robust way to do it 'properly'

Edit: use of tail removes the leading blank line.

[GenoMax]

No need to cat the file. Just the sed part should be enough.

[Joe]

Yeah I know, it's just how I prefer to do it. You get to see the file, then can just redirect the file with > if it looks right. sed -i makes me nervous :P

Answer 2

[nepgorkhey]

a short python script like the following may work for you

for lines in f:
     if lines[0]=='>':
             print lines
    else:
             lines=lines+'\n'
             print lines