Getting FASTA collapsed reads

[vilperte]

Hello!

I need to convert an uncollapsed FASTA file in a collapsed one.

I managed to do that using a script from the miR-PREFeR tool for miRNA prediction. However, I need them to look like this: >t0000001 15, >t0000002 45, and so on, but I only managed to get something like >t1 15, >t2 45, and so on.

Does anyone know how to do that (any script or tool)?

Thanks!

Vinicius

[GenoMax]

A modification using Phillip's answer from (http://seqanswers.com/forums/showpos...19&postcount=3) should do the trick.

Try this.

$ perl -i.bak -pe 'BEGIN{$N="0000001"}next unless /^>/;s/(>\S+)/>t$N/;$N++' your_file