Fasta Conversion

Question

[Syawash]

Hi there, Is there away change identifiers in a fasta file. For examplt from

>fastsdde135667667
actgcagtctga
>fgdte12875
actggact

to

>Seq1
actgcagtctga
>Seq2
actggact

Answer 1

[Pierre Lindenbaum]

use awk:

awk '/^>/ { printf(">Seq%d\n",(++i)); next;} { print }' < input.fa > output.fa

Ex:

echo ">fastsdde135667667
actgcagtctga
>fgdte12875
actggact" | awk '/^>/ { printf(">Seq%d\n",(++i)); next;} { print }'

>Seq1
actgcagtctga
>Seq2
actggact

[Eric Normandeau]

Hi Pierre. Just curious if you can add padding with zeroes simply with awk. Eg: seq1 --> seq0001, seq253 --> seq0253. Happy New Year :)

[Pierre Lindenbaum]

@Eric, yes that works like the std C printf: printf(">Seq%03d\n",(++i))

[Eric Normandeau]

@Pierre, nice! Thanks. Have to learn more C and C++ some time.

Answer 2

[Daniel]

also, this:

#!/usr/bin/perl

$count =1;

while (<>){
        if (s/^>.*/>Seq$count/){;
        $count++;
        }
        print;
}

>Seq1
actgcagtctga
>Seq2
actggact

Answer 3

[Martin A Hansen]

With Biopieces and add_ident:

read_fasta -i input.fa | add_ident -k SEQ_NAME -p Seq | write_fasta -o output.fa -x