Adding count number at the end of header in a fasta file

[garethboy]

Hi there. I would like to add count number at the end of the head, from this:

>ECOLI
ACTGCGTAGTCGTACTATGCAACACACGTGTGTATGCT
>ECOLI
ACGTTAGTTTCGCGTAGTCGTATGCTACGATCGTAGCA
>ECOLI
ACGTGTGCAACCTGCACTGTGCTAGCACGACACAACGTG
.
.
.
>ECOLI
ATGTGTACGTAGCTAGCTAGCATCGATCTGCTAGCATGC
>ECOLI
GTCGATGCTGCTCGATCGATCGATCGTACGATCGATGATC
become this:

>ECOLI|00000001
ACTGCGTAGTCGTACTATGCAACACACGTGTGTATGCT
>ECOLI|00000002
ACGTTAGTTTCGCGTAGTCGTATGCTACGATCGTAGCA
>ECOLI|00000003
ACGTGTGCAACCTGCACTGTGCTAGCACGACACAACGTG
.
.
.
>ECOLI|00000099
ATGTGTACGTAGCTAGCTAGCATCGATCTGCTAGCATGC
>ECOLI|00000199
GTCGATGCTGCTCGATCGATCGATCGTACGATCGATGATC

Can anyone guide me how to add the count number like the above?

Thank you very much.

[dariober]

You could use bioawk for this:

bioawk -c fastx '{print ">" $name sprintf("|%05d", NR) "\n" $seq}' test.fa

>ECOLI|00001
ACTGCGTAGTCGTACTATGCAACACACGTGTGTATGCT
>ECOLI|00002
ACGTTAGTTTCGCGTAGTCGTATGCTACGATCGTAGCA
>ECOLI|00003
ACGTGTGCAACCTGCACTGTGCTAGCACGACACAACGTG
...

[pmiguel]

perl -i.bak -pe 'BEGIN{$N="00000001"}next unless /^>/;s/(>\S+)/$1|$N/;$N++' t.fa

Changes the sequences in t.fa from:

>ECOLI
ACTGCGTAGTCGTACTATGCAACACACGTGTGTATGCT
>ECOLI
ACGTTAGTTTCGCGTAGTCGTATGCTACGATCGTAGCA
>ECOLI
ACGTGTGCAACCTGCACTGTGCTAGCACGACACAACGTG


to

>ECOLI|00000001
ACTGCGTAGTCGTACTATGCAACACACGTGTGTATGCT
>ECOLI|00000002
ACGTTAGTTTCGCGTAGTCGTATGCTACGATCGTAGCA
>ECOLI|00000003
ACGTGTGCAACCTGCACTGTGCTAGCACGACACAACGTG


It also makes a handy back up file saved as "t.fa.bak" just in case you regret the modifications you've made to the original file.

--
Phillip

[garethboy]

dear all, thanks. it is very useful. :-)