| Posted on 2009-05-12 16:06:47-07 by pauleym |
| Using Getopt::Declare |
|
Hi,
I have been trying to use Getopt::Declare but without success. Listed below is a small program that attempts to use the module. (Note that in the code for each parameter definition one or more tab characters separate it and the description; all other whitespace in the specification are spaces.) After that are the error messages I get when I try to run my program. (Note that if I use test.pl -v I don't get the message "In verbose mode.") I've read through the Getopt::Delcare documentation many times and it seems that the format of my specification is correct so I don't understand why it is not working. Any help or suggestions would be greatly appreciated.
Mark
###################################################################################################
+#
#! /usr/bin/perl -w
use strict; # Prevent unsafe constructs
use Getopt::Declare; # Processes command-line parameters (for usage
# search http://www.cpan.org for Getopt::Declare)
use Bio::Seq; # Use BioPerl packages
use Bio::SeqIO;
# The parameter definition consists of a leading flag or parameter variable,
# followed by any number of parameter variables or punctuators, optionally
# separated by spaces. The parameter definition is terminated by the first
# tab that is encountered after the start of the parameter definition. At least
# one trailing tab must be present.
$specification = q(
-i <FILE> Input filename
--input <FILE> [ditto] (long form)
-o <FILE> Output filename
--output <FILE> [ditto] (long form)
-c Process chaperonin proteins only
--chap [ditto] (long form)
-n Process non-chaperonin proteins only
--nonchap [ditto] (long form)
-a Process all proteins
--all [ditto] (long form)
[mutex: -c --chap -n --nonchap -a -all]
# Specifies mutually exclusive options
-v Verbose mode (echos output to screen)
--verbose [ditto] (long form)
[nocase] # Everything is case insensitive
-- End of arguments
{ finish }
);
my $args = Getopt::Declare->new($specification);
# Determine verbosity
my $verbose = 0; # Verbose flag (assumed false)
if (($args->{'v'}) or ($args->{'--verbose'})) {
$verbose = 1;
print "In verbose mode."
}
my $inFile = ""; # Input filename
my $outFile = ""; # Output filename
# Get input filename (either from command-line or via user prompt)
if ($args->{'-i'}) {
$inFile = $args->{'-i'}{'<FILE>'};
} elsif ($args->{'--input'}) {
$inFile = $args->{'--input'}{'<FILE>'};
} else {
print "Input filename for reading: ";
$inFile = <STDIN>;
chomp $inFile;
}
# Get output filename (either from command or via user prompt)
if ($args->{'-o'}) {
$inFile = $args->{'-o'}{'<FILE>'};
} elsif ($args->{'--output'}) {
$inFile = $args->{'--output'}{'<FILE>'};
} else {
print "Output filename for writing: ";
$outFile = <STDIN>;
chomp $outFile;
}
# Open input file (a FASTA file)
my $seqio_obj = Bio::SeqIO->new(-file => $inFile,
-format => "fasta" );
# Open output file (simple flatfile)
unless (open(OUTPUT, ">$outFile")) {
die "Cannot open $outFile for writing. Stopped.";
}
# Exit the program gracefully
exit(0);
###################################################################################################
mpauley@mpauley-desktop:~/projects/yellowstone/chaperones$ ./test.pl --verbose -i microbes_20090422
+.fna -o testout.tab
Name "main::OUTPUT" used only once: possible typo at ./test.pl line 90.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/perl/5.8.8/Getopt/Dec
+lare.pm line 544.
Use of uninitialized value in hash element at /usr/local/share/perl/5.8.8/Getopt/Declare.pm line 86
+.
Use of uninitialized value in hash element at /usr/local/share/perl/5.8.8/Getopt/Declare.pm line 86
+.
Use of uninitialized value in hash element at /usr/local/share/perl/5.8.8/Getopt/Declare.pm line 86
+.
Use of uninitialized value in hash element at /usr/local/share/perl/5.8.8/Getopt/Declare.pm line 87
+.
Use of uninitialized value in hash element at /usr/local/share/perl/5.8.8/Getopt/Declare.pm line 87
+.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/perl/5.8.8/Getopt/Dec
+lare.pm line 539.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/perl/5.8.8/Getopt/Dec
+lare.pm line 539.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/perl/5.8.8/Getopt/Dec
+lare.pm line 539.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/perl/5.8.8/Getopt/Dec
+lare.pm line 539.
Use of uninitialized value in concatenation (.) or string at /usr/local/share/perl/5.8.8/Getopt/Dec
+lare.pm line 539.
Can't use string ("microbes_20090422.fna") as a HASH ref while "strict refs" in use at ./test.pl li
+ne 65.
In verbose mode.
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