Question

In a perl script, I need to replace several strings. At the moment, I use:

$fasta =~ s/\>[^_]+_([^\/]+)[^\n]+/\>$1/g;

The aim is to format in a FASTA file every sequence name. It works well in my case so I don’t need to touch this part. However, it happens that a sequence name appears several times in the file. I must not have at the end twice – or more – the same sequence name. I thus need to have for instance:

seqName1
seqName2
etc.

(instead of seqName, seqName, etc.)

Is this possible to somehow process differently every occurrence automatically? I don’t know how many sequence there are, if there are similar names, etc. An idea would be to concatenate a random string at every occurrence for instance, hence my question.

Many thanks.

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John perfectly solved it and chepner helped with the smart idea to avoid conflicts, here is the final result:

$fasta =~ s/\>[^_]+_([^\/]+)[^\n]+/
    sub {
        return '>'.$1.$i++;
    }->();
/eg;

Many many thanks.

Answer 1

I was actually trying to do something like this the other day, here’s what I came up with

$fasta =~ s/\>[^_]+_([^\/]+)[^\n]+/

    sub {

        # return random string

    }->();

/eg;

the \e modifier interprets the substitution as code, not text. I use an anonymous code ref so that I can return at any point.