Add a sequence name!

Question

[fufuyou]

Hi, I get my sequence files like this

TAACAGTGGGTCGAGATAAGGAC    1
CGCCCGGACGTCAGAGAAAAAGGTGCCAGCGCGGCGCAGAGAATGGAATT    1
TTAGTATGACGGGCTGACACGAGA    3

I want to add a sequence name at each sequence file as like:

>seq000001 1
TAACAGTGGGTCGAGATAAGGAC
>seq000002 1
CGCCCGGACGTCAGAGAAAAAGGTGCCAGCGCGGCGCAGAGAATGGAATT
>seq000003 3

Thanks, Fuyou

[John]

You seem to enjoy using custom-made formats :P

Where does the sequence name data come from Fuyou?

[fufuyou]

Hi John, Thanks, The seq name only need randomly name. It like I have wrote name, seq000001,seq000002,seq000003. Thanks

Answer 1

[venu]

Assuming every sequence is of one line and you need to create the sequence headers

wc -l sequences.fa

Lets say you've got 100

for i in {1..100}; do echo "Seq000"$i >> ids.txt; done

paste ids.txt sequences.fa | awk '{print $1"-"$3"\t"$2}' | tr '\t' '\n' | sed 's/^/>/;n' | sed 's/-/ /g' > new_file.fa

Output

>seq0001 1
CAGTGGGTCGAGATAAGGAC
>seq0002 1
CGCCCGGACGTCAGAGAAAAAGGTGCCAGCGCGGCGCAGAGAATGGAATT
>seq0003 3
TTAGTATGACGGGCTGACACGAGA

[michael.ante]

Playing awk-golf:

awk '{printf ">seq%06d %d\n%s\n" , NR,$2,$1}' sequences.fa > new_sequence.fa

This takes the line number (NR) as the number for the seq-id, paste the last number in the fasta-header, and prints the sequence in a separate line.

All under the assumption, that you have per line one sequence followed by the number.

[venu]

Intelligent way of using awk.

[fufuyou]

Thanks Michael, It is great. Fuyou

[John]

This is great venu - thank you :)