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Re: Shell calling input FASTA file

by biohisham (Priest)
on Oct 16, 2014 at 14:01 UTC ( #1104057=note: print w/replies, xml ) Need Help??


in reply to Shell calling input FASTA file

How does a fasta header in your input file look like? I tried to reproduce the behavior you are alluding to by using your code and a couple of fasta sequences, but your code seems to be working just fine.

A side notice on your first code (open FILE, "mRNA.fa" or die $!;). That open statement lacks telling it what mode you want to open mRNA.fa into. It is a good practice to decide if you want to open your file for input, output or appending. The second open statement from the newer code is a better way of opening a file since you have instructed open on the type of mode you want to open your file in.


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