Using awk:

awk '/^>/ {printf("\n%s\n",$0);next; } { printf("%s",$0);}  END {printf("\n");}' < file.fa

>gi|321257144|ref|XP_003193485.1| flap endonuclease [Cryptococcus gattii WM276]
MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFYRTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNEECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKKMPISEIHLDVALRDLEMSMDQFIELCILLGCDYLEPCKGIGPKTALKLMREHGTLGKVVEHIRGKMAEKAEEIKAAADEEAEAEAEAEKYDSDPENEEGGETMINSDGEEVPAPSKPKSPKKKAPAKKKKIASSGMQIPEFWPWEEAKQLFLKPDVVNGDDLVLEWKQPDTEGLVEFLCRDKGFNEDRVRAGAAKLSKMLAAKQQGRLDGFFTVKPKEPAAKDAGKGKGKDTKGEKRKAEEKGAAKKKTKK
>gi|321473340|gb|EFX84308.1| hypothetical protein DAPPUDRAFT_47502 [Daphnia pulex]
MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYRTIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKMPIKEFHLDKILDGLSYTMDEFIDLCIMLGCDYCDTIKGIGAKRAKELIDKHRCIEKVIENLDTKKYTVPENWPYQEARRLFKTPDVADAETLDLKWTQPDEEGLVKFMCGDKNFNEERIRSGAKKLCKAKTGQTQGRLDSFFKVLPSSKPSTPSTPASKRKVGCIIYLFLYF

Edit: for Window$.

• Download ubuntu http://www.ubuntu.com/download
• burn a cd with ubuntu
• reboot your computer with this CD
• install ubuntu

:-)

here is a quick and simple perl one-liner:

perl -pe '/^>/ ? print "\n" : chomp' in.fasta > out.fasta

which will output an empty header line. you could use tail (which is faster than sed) to remove it:

perl -pe '/^>/' ? print "\n" : chomp' in.fasta | tail -n +2 > out.fasta

EDIT: even easier (do not use!):

perl -pe 'chomp unless /^>/' in.fasta > out.fasta

EDIT2: this last one liner does not work as expected. use this one instead, which performs inside a single perl call all the logic needed in all lines but the first one by using perl's $. internal line counter variable:

perl -pe '$. > 1 and /^>/ ? print "\n" : chomp' in.fasta > out.fasta

Also a quick & dirty solution with Perl... (fa2oneline.pl)

#!/usr/bin/perl -w
use strict;

my $input_fasta=$ARGV[0];
open(IN,"<$input_fasta") || die ("Error opening $input_fasta $!");

my $line = <IN>; 
print $line;

while ($line = <IN>)
{
chomp $line;
if ($line=~m/^>gi/) { print "\n",$line,"\n"; }
else { print $line; }
}

print "\n";

then run:

perl fa2oneline.pl sample.fa > out.fa

Result :

>gi|321257144|ref|XP_003193485.1| flap endonuclease [Cryptococcus gattii WM276]
MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFYRTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNEECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKKMPISEIHLDVALRDLEMSMDQFIELCILLGCDYLEPCKGIGPKTALKLMREHGTLGKVVEHIRGKMAEKAEEIKAAADEEAEAEAEAEKYDSDPENEEGGETMINSDGEEVPAPSKPKSPKKKAPAKKKKIASSGMQIPEFWPWEEAKQLFLKPDVVNGDDLVLEWKQPDTEGLVEFLCRDKGFNEDRVRAGAAKLSKMLAAKQQGRLDGFFTVKPKEPAAKDAGKGKGKDTKGEKRKAEEKGAAKKKTKK
>gi|321473340|gb|EFX84308.1| hypothetical protein DAPPUDRAFT_47502 [Daphnia pulex]
MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYRTIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKMPIKEFHLDKILDGLSYTMDEFIDLCIMLGCDYCDTIKGIGAKRAKELIDKHRCIEKVIENLDTKKYTVPENWPYQEARRLFKTPDVADAETLDLKWTQPDEEGLVKFMCGDKNFNEERIRSGAKKLCKAKTGQTQGRLDSFFKVLPSSKPSTPSTPASKRKVGCIIYLFLYF

Biopieces (www.biopieces.org) is another way:

read_fasta -i file.fna | write_fasta -x

Cheers,
Martin

Python version to convert multi-line to two-line fasta format. It also converts multiple files. Output directory will have all the files with _twoline.fasta as suffix.

from Bio import SeqIO
import os
import re
import argparse

def multi2linefasta(indir,outdir,filelist):
    for items in filelist:
        mfasta = outdir +"/"+re.sub('\..*','',items)+'_twoline.fasta'
        ifile = open(indir+'/'+items,'rU')
        with open(mfasta, 'w') as ofile:
            for record in SeqIO.parse(ifile, "fasta"):
                sequence = str(record.seq)
                ofile.write('>'+record.id+'\n'+sequence+'\n')


if __name__ == '__main__':
    parser = argparse.ArgumentParser(description='Convert multiple files of multi-line fasta into two-line fasta format')
    parser.add_argument('-i',type=str,dest='ind',required=True,help="Input directory where all the fasta files are present")
    parser.add_argument('-o',type=str,dest='outd',required=True,help="Ouput directory")
    parser.add_argument('-f',type=str,dest='ffiles',required=True,help="Comma seperated fasta file names without spaces")
    args = parser.parse_args()
    print (args)
    filelist = args.ffiles.split(',')
    if not os.path.exists(args.outd):
        os.makedirs(args.outd)
    multi2linefasta(args.ind,args.outd,filelist)

To run, save the above code to convertfasta.py file

python convertfasta.py -i "/path/to/inputfolder/" -o "/path/to/outputfolder/" -f "file1.fasta,file2.fasta,file3.fasta"

It seems that seqtk (https://github.com/lh3/seqtk) can be used for this task, although the webpage only mentions multiline fastq. The command to give is simply (I am using Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz, but one can use any fasta or gzipped fasta):

seqtk seq -l0 Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz | gzip > Homo_sapiens.GRCh37.dna.primary_assembly.singleLines.fa.gz

For a quick proof that this works, try:

zcat Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz | head -n10 | seqtk seq -l0 | cat -A

Kent source's faToTab. I'm sure EMBOSS has something for this as well. If you are on a Windows machine, I'd just use Galaxy's fasta2tab.

use strict;
use warnings;
use Bio::SeqIO;

my $in  = Bio::SeqIO->new(-file => "myseq.fasta" , '-format' => 'Fasta');

while ( my $seq = $in->next_seq ) {
    print ">",$seq->id()," ",$seq->desc(),"\n",$seq->seq(),"\n";
}

Output:

>gi|321257144|ref|XP_003193485.1| flap endonuclease [Cryptococcus gattii WM276]
MGIKGLTGLLSENAPKCMKDHEMKTLFGRKVAIDASMSIYQFLIAVRQQDGQMLMNESGDVTSHLMGFFYRTIRMVDHGIKPCYIFDGKPPELKGSVLAKRFARREEAKEGEEEAKETGTAEDVDKLARRQVRVTREHNEECKKLLSLMGIPVVTAPGEAEAQCAELARAGKVYAAGSEDMDTLTFHSPILLRHLTFSEAKKMPISEIHLDVALRDLEMSMDQFIELCILLGCDYLEPCKGIGPKTALKLMREHGTLGKVVEHIRGKMAEKAEEIKAAADEEAEAEAEAEKYDSDPENEEGGETMINSDGEEVPAPSKPKSPKKKAPAKKKKIASSGMQIPEFWPWEEAKQLFLKPDVVNGDDLVLEWKQPDTEGLVEFLCRDKGFNEDRVRAGAAKLSKMLAAKQQGRLDGFFTVKPKEPAAKDAGKGKGKDTKGEKRKAEEKGAAKKKTKK

>gi|321473340|gb|EFX84308.1| hypothetical protein DAPPUDRAFT_47502 [Daphnia pulex]
MGIKGLTQVIGDTAPTAIKENEIKNYFGRKVAIDASMSIYQFLIAVRSEGAMLTSADGETTSHLMGIFYRTIRMVDNGIKPVYVFDGKPPDMKGGELTKRAEKREEASKQLVLATDAGDAVEMEKMNKRLVKVNKGHTDECKQLLTLMGIPYVEAPCEAEAQCAALVKAGKVYATATEDMDSLTFGSNVLLRYLTYSEAKKMPIKEFHLDKILDGLSYTMDEFIDLCIMLGCDYCDTIKGIGAKRAKELIDKHRCIEKVIENLDTKKYTVPENWPYQEARRLFKTPDVADAETLDLKWTQPDEEGLVKFMCGDKNFNEERIRSGAKKLCKAKTGQTQGRLDSFFKVLPSSKPSTPSTPASKRKVGCIIYLFLYF

You can open the merged sequences in the UGENE Sequence View. To do it:

1. Select "File>Open as" in the main UGENE menu.
2. Select the "FASTA" format.
3. Select "Merge sequences into a single sequence to show in the sequence viewer".

By default, UGENE will show the sequence itself, the complementary sequence and translations. It looks like here.

If required, you can export the merged sequence into a new file.

Hi

Hope this works

awk 'BEGIN{RS=">"}NR>1{sub("\n","\t"); gsub("\n",""); print RS$0}' file

You may have found a solution already, but here's a quick method: Open your file in a text editor (Notepad++?), find \r\n and replace it with blank, then type > in 'find what' and replace it with \r\n :) Hope it works/helps.

Hi

Short answer:

Use seqtk as follows:

$ seqtk seq multi-line.fasta > single-line.fasta

Explained:

A toy example in multi-line format:

$ head -n5 celegans_chr1.fa
>gi|449020133|emb|BX284601.5| Caenorhabditis elegans Bristol N2 genomic chromosome, I
GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT
AAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGC
CTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA
GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCT

How to easily convert to single-line fasta (I only print head -c 170 as it would print the whole chromosome otherwise):

$ seqtk seq celegans_chr1.fa | head -c 170
>gi|449020133|emb|BX284601.5| Caenorhabditis elegans Bristol N2 genomic chromosome, I
GCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAAGCCTAA

So you can simply redirect the stdout to a file as follows:

$ seqtk seq celegans_chr1.fa > celegans_chr1_single-line.fa

You may also use a file compressor like gzip to compress the file.