I am a novice in this field. Please help me identify the mistake in this code to use GetOptions. I am using Windows OS (Win8.1)
#!/C:/Perl64/bin/perl
require 5.16.3;
# use strict;
use warnings;
undef $/;
use Getopt::Long;
my $file= '';
GetOptions('filename|f=s' => \$file);
# I am keeping a Seq file in the same folder
open(IN, $file) or die "Cannot Read $file: $file$!\n";
my $data= ;
my $a= ($data =~ tr/A//);
my $t= ($data =~ tr/T//);
my $g= ($data =~ tr/G//);
my $c= ($data =~ tr/C//);
my$Total= ($a+$t+$g+$c);
my $gc= (($g+$c)/($Total))*100;
print "A: $a\n";
print "T: $t\n";
print "G: $g\n";
print "C: $c\n";
print "Total: $Total\n";
print "GC-Content: $gc\n";
printf "GC-Content: %6.3f%\n", $gc."\n";
@ Dr Hector Candela,
the first % is for floating point data conversion, the last% is to indicate percent. This part is OK. The mistake is somewhere in the GetOpt() portion, which I am unable to identify. Please point out the mistake.
printf "GC-Content: %6.3f %% \n", $gc
Use this statement instead of your last statement. 2 changes are there-
1) an extra % symbol is there due to which invalid conversion in printf warning occurs
2) Remove '.' and add ','
I am running your script (including the correction) using Strawberry Perl in a PC running Windows with no errors.
Perhaps you are not specifying the name of the sequence file correctly?
perl name_of_script.pl -f name_of_sequence_file
or
perl name_of_script.pl -filename name_of_sequence_file
@ Hector Candela & Vandana Kumari, thanks a lot for your kind help.
I will run the code as suggested.
@ Hector Candela, it is still not working. I am keeping both .pl and .seq files in the same folder.
Please vide attachment for the PERL prompt when I run the .pl file.
It is accepting "perl TestModule.pl -f DNA.seq" however the cursor is moving to next line and blinking indefinitely.
No response is obtained.
Please reply.
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