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fasta file to tab delimited file

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?

sequence
• 18,401 views • link
updated by scchess scchess • written by nakanomasayuki265 • nakanomasayuki265

2 answers

Sure, just use awk:

$ awk 'BEGIN{RS=">"}{print "#"$1"\t"$2;}' in.fa | tail -n+2 > out.txt
• 0 views • link
written by Alex Reynolds Alex Reynolds

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

• 0 views • link
written by 5heikki 5heikki

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

• 0 views • link
written by yangzituo • yangzituo

like:

seq1  AAAATTTT
seq2 CCCCGGGG

convert it back to:

>seq1
AAAATTTT
>seq2
CCCCGGGG

Thanks~

• 0 views • link
written by yangzituo • yangzituo

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

seqkit fx2tab myFASTA >  myTAB
• 1 views • link
updated by finswimmer finswimmer • written by scchess scchess

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
• 1 views • link
written by Ram Ram

My sample command did indeed converted FASTA to TSV.

• 1 views • link
written by scchess scchess

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.

• 1 views • link
written by Ram Ram

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

• 1 views • link
written by scchess scchess

How so? Can you explain please?

• 1 views • link
written by Ram Ram 
$ 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
• 1 views • link
written by cpad0112 cpad0112

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
• 1 views • link
written by finswimmer finswimmer

Thank you ! This is great !!

• 0 views • link
written by lagartija lagartija

@ 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

• 1 views • link
written by cpad0112 cpad0112

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