Fasta to text format

Question

[clarkanna150]

Is there a quick way to convert fasta formats into text files? I need to convert whole genome sequences into .txt files for some software I am using, so need to remove scaffold assignments, so that the structure is the species name, followed by the entire sequence on "one line".

[Ram]

You're describing a custom plain text format, possibly space or tab separated with the species in the first field and the whole sequence in the second field, correct?

Where would you get the species name from?

[clarkanna150]

Yes that is correct. Pref space delimited, with species name deriving from the 'filename' that the sequence is from.

[GenoMax]

Use this code courtesy of @Pierre. You can then cat the linearized files together. Change \t to space if you need that :

Linearize a fasta sequence

awk -f linearizefasta.awk < input.fa

or

awk '/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;} {printf("%s",$0);} END {printf("\n");}' < input.fa

Format back to fasta

tr "\t" "\n" < linearized.tsv

if you know your fasta header have a length < 60

tr "\t" "\n" < linearized.tsv | fold -w 60

view raw README.md hosted with ❤ by GitHub

	/^>/ {printf("%s%s\t",(N>0?"\n":""),$0);N++;next;}
	{printf("%s",$0);}
	END {printf("\n");}

view raw linearizefasta.awk hosted with ❤ by GitHub