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
[download]

However, my instructor wants the file to be called using command line prompt

perl <programName.pl> <input file>
[download]

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>;
[download]

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?).
[download]

Any advice would be greatly appreciated! Thank you!

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.