How to reshape a fasta file?

Question

[gbl1]

Hello,

I've got some sequences shaped as

>Sj-D-P_M0276n4:119:000000000-C5R9K:1:1106n:1548n9:8n8n42 1:N:0:7
CTCAGAGCCAGGGTGCCACAGGTAAGAGTTACCTAAACTCAACATCCACGCTCTTTTTTGACCGCATGTC
TGAAACTTGAAGGAATTCCACCATTGCTTGTAGTCATCCTGAGTCAAATTTGCAGTTGTCTCACCACATG
TATGACCACCAGAGCCCTGGCCCTTCTCCATGTCCCGTGCATACCGCACGCCTCGCCGCTATTACCGTGC
CGAGCCACCGCTGTCCCGATCGAGTCTCAAGGGCCGCAAACCCACACCACTCAACCCCTGCTGCAAGGTG
AGGACCCGCAACTCGCTGT

I would like to remove the back to lines in the sequences (but not in the names) like:

>Sj-D-P_M0276n4:119:000000000-C5R9K:1:1106n:1548n9:8n8n42 1:N:0:7    
CTCAGAGCCAGGGTGCCACAGGTAAGAGTTACCTAAACTCAACATCCACGCTCTTTTTTGACCGCATGTCTGAAACTTGAAGGAATTCCACCATTGCTTGTAGTCATCCTGAGTCAAATTTGCAGTTGTCTCACCACATGTATGACCACCAGAGCCCTGGCCCTTCTCCATGTCCCGTGCATACCGCACGCCTCGCCGCTATTACCGTGCCGAGCCACCGCTGTCCCGATCGAGTCTCAAGGGCCGCAAACCCACACCACTCAACCCCTGCTGCAAGGTGAGGACCCGCAACTCGCTGT

How to proceed?

Thanks in advance

[lieven.sterck]

have you looked around for a (possible) solution? This has been covered several times before. try googling on something like "reformat fasta file to single line", that will give you numerous options.

one of the results will be Multiline Fasta To Single Line Fasta for instance.

[Joe]

The keyword you’re looking for here is likely “linearising fasta”

[gbl1]

Thanks :)

I had looked for "reshape fasta" nothing out… Well, a non-native issue

[GenoMax]

This is the thread you were looking for: A: Multiline Fasta To Single Line Fasta

Answer 1

[JC]

perl -pe 's/\n// unless (/>/)' < FASTA > LINEARFASTA