Shell calling input FASTA file

JoUthoff has asked for the wisdom of the Perl Monks concerning the following question:

I am writing a perl program to find the longest open reading frames in a mRNA.fa sequence. I can easily do this by calling the file from the script using:

open FILE, "mRNA.fa" or die $!; # Opens mRNA, assoicates FILE
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However, my instructor wants the file to be called using command line prompt

perl <programName.pl> <input file>
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Now I have tried using the command ARGV to pull the filename from the bash:

my $file = $ARGV[0];
open (my $mRNAfile, "<", $file) or die $!; 
my @mRNAdata = ( ); # initalizes the variables of array
@mRNAdata = <$mRNAfile>;
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When I run this, I receive compilation errors for each of the 100 sequences saying:

"Number found where operator expected at - line 1, near "Sequence 1" (
+Do you need to predeclare Sequence?).
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Any advice would be greatly appreciated! Thank you!

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Re: Shell calling input FASTA file by AnomalousMonk (Archbishop) on Oct 16, 2014 at 03:44 UTC
Just sneaking suspicion and wild surmise here, can't test this, but your command line is something like `perl programName.pl mRNA.fa` and not `perl <programName.pl> <mRNA.fa>` isn't it? (The `< >` angle brackets are just metasyntactic delimiters. (Update: Well, as used by your instructor, they're just metasyntactic delimiters. On a command line, of course, they're re-direction operators — a very significant difference!))	[reply] [d/l] [select]
Re: Shell calling input FASTA file by biohisham (Priest) on Oct 16, 2014 at 14:01 UTC
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. A 4 year old monk	[reply] [d/l] [select]


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