fasta file to tab delimited file

Question

[nakanomasayuki265]

I want to change the format of the fasta file.

>Name
AAAAAAAAAAAAAAAAAAAAAAAAA
>Fasta
BBBBBBBBBBBBBBBBBBBBBBBBBB
·
·
·

Fasta files are in a state with no line breaks except for> lines.

I would like to do this as tab delimited.

#Name AAAAAAAAAAAAAAAAAAAAAAAAA
#Fasta BBBBBBBBBBBBBBBBBBBBBBBBB
#·
#·
#·

What kind of commands and scripts are there? Could you please tell me?

[Brian Bushnell]

This sounds like an XY problem. Can you explain what you are trying to accomplish?

Answer 1

[Alex Reynolds]

Sure, just use awk:

$ awk 'BEGIN{RS=">"}{print "#"$1"\t"$2;}' in.fa | tail -n+2 > out.txt

[5heikki]

Alternative: awk 'BEGIN{RS=">";OFS="\t"}NR>1{print "#"$1,$2}' inFile > outFile

[yangzituo]

Hey, do you know how to change tab delimited back to fasta format?

[yangzituo]

like:

seq1  AAAATTTT
seq2 CCCCGGGG

convert it back to:

>seq1
AAAATTTT
>seq2
CCCCGGGG

Thanks~

[shenwei356]

seqkit

seqkit tab2fx xxx.tab > xxx.fasta

Answer 2

[scchess]

Please use the seqkit tool. The accepted solution wouldn't work for multiple lines, so it should be ignored.

seqkit fx2tab myFASTA >  myTAB

[Ram]

will not work for multiple lines in FASTQ

• FASTQ has only one sequence line (of significance at least)
• OP asked FASTA to TSV, not FASTQ to TSV

[scchess]

My sample command did indeed converted FASTA to TSV.

[Ram]

Yes, but the accepted answer does work on multiple lines, unless I'm missing something. RS=> should take care of not separating records by \n.

[scchess]

The accepted answer had "tail -n+2 ", it wouldn't work for multiple lines.

[Ram]

How so? Can you explain please?

[cpad0112]

$ cat test.fa 
>Name
AAAAAAAAAAA
AAAAAA

>Fasta
BBBBBBBBBBBBBB
BBBBB
B
BBBBBB

$ awk 'BEGIN{RS=">"}{print "#"$1"\t"$2;}' test.fa | tail -n+2
#Name   AAAAAAAAAAA
#Fasta  BBBBBBBBBBBBBB

$ seqkit fx2tab test.fa
Name    AAAAAAAAAAAAAAAAA   
Fasta   BBBBBBBBBBBBBBBBBBBBBBBBBB

or a simple case:

$ awk 'BEGIN{RS=">"}{print "#"$1"\t"$2;}' test.fa | tail -n+2 
#Name   AAAAA
#Fasta  B

$ cat test.fa 
>Name
AAAAA A

>Fasta
B
BBBBBB

[finswimmer]

This should work for multiline fasta:

$ awk -v RS=">" -v ORS="\n" -v OFS="" '{$1="#"$1"\t"}1' test.fa|tail -n+2
#Name   AAAAAAAAAAAAAAAAA
#Fasta  BBBBBBBBBBBBBBBBBBBBBBBBBB

$ cat test.fa   
>Name
AAAAAAAAAAA
AAAAAA

>Fasta
BBBBBBBBBBBBBB
BBBBB
B
BBBBBB

[lagartija]

Thank you ! This is great !!

[cpad0112]

@ SmallChess tail -n+2 removes unwanted first line. However as you mentioned, code doesn't work for multi line fasta or fasta with gaps in the sequence