I am trying to write a perl one liner that...

You start with a problem statement who's solution is meaningless in the real world. Perl Golf is an interesting game, but I'm not sure that you really understand that you are playing golf? If this is not a golf competition, then why on earth would you write such code?

I do not see how this code makes any sense: 

   chomp;
   @a=split(/\t/);
   $a[0]=~s/\s+//g;
   $a[1]=~s/\s+//g;
   $a[2]=~s/\s+//g;
   $a[3]=~s/\s+//g;

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This code has nothing to do with the FASTA spec.

I highly recommend using the BIO Perl modules. The FastA format is simple and I wrote one parser at Re: Bio perl package - I think I've written more. But even so, I don't recommend my code as the end-all and be-all.

In reply to Re: Printing all lines of a file using a perl one liner by Marshall
in thread Printing all lines of a file using a perl one liner by la

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