Not actually a fix to your code, but a slightly different approach, would be to temporarily store each FASTA record in a hash using the complete header as a key. This way you can check for existence of a known header and print out the records together.

I haven't tested it, but the problem you are getting looks like it could be a buffering issue? If you ++$|; # turn off buffering, the issue might go away, but I still think i would go with the hash approach as it doesn't rely on the records being in the same order etc... HTH

Just a something something...

In reply to Re: combine 2 fasta files into 1 by BioLion
in thread combine 2 fasta files into 1 by newbie25

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