I'm using Getopt::Long::Subcommand to parse the command line arguments.
But I found that in some of Perl versions. This module has incorrect behavior.
For example if I run ./ViewBS BisNonConvRate --sample bis_WT.tab.gz,WT. I expect the output as below:
Subcommand: BisNonConvRate
Sample list: bis_WT.tab.gz,WT
In perl-v5.18.2, it works fine. I got the output I expected. But in perl-v5.24.1, it does NOT. I got the output shown as below:
Subcommand: BisNonConvRate
Sample list:
I checked version of Getopt::Long::Subcommand. Both of them are the same version (0.102).
Could anyone help on this issue? Thanks in advance.
Here is how I configure the perl environment:
perlbrew install perl==5.24.1 ## or perl==5.18.2
perlbrew use perl-5.24.1
perlbrew install-cpanm
cpanm Getopt::Long::Subcommand
cpanm Bio::DB::HTS::Tabix
cpanm Bio::SeqIO
Here is my code using Getopt::Long::Subcommand in 'ViewBS':
#!/usr/bin/env perl
#!/usr/bin/perl --
####################################################################
# ViewBS - Tools for exploring and visualizing bisulfite sequencing
# (BS-seq) data.
####################################################################
use strict;
use warnings;
use Getopt::Long::Subcommand;
use Pod::Usage;
use File::Basename;
use Cwd qw(abs_path);
use Benchmark;
my $t_stt = Benchmark->new;
#use FindBin;
#use lib "$FindBin::Bin";
$|++; # Do not buffer output
#$| = 1; # Do not buffer output
#Self written libraries.
## Package written by Shanshan Huang
use lib dirname(abs_path $0) . '/lib'; #include seft written packages in @INC.
my $main_path = dirname(abs_path $0);
my %opts; ## store the values for common parameters
my %opts_subcmd; ### store the values for sub command parameters
### Return hash structure, with these keys: success, subcommand (array of str) by GetOptions
my $resOpt = &processCMD();
my ($sub_cmd) = @{$resOpt->{subcommand}};
print "\nSubcommand: $sub_cmd\n";
if($sub_cmd eq "BisNonConvRate"){
print "Sample list: @{$opts_subcmd{sample}}\n";
}
sub processCMD{
$resOpt = GetOptions( # Return hash structure, with these keys: success, subcommand (array of str)
## common options recognized by all subcommands
options => {
'help|h|?' => \$opts{help},
'version|v' => \$opts{version},
'verbose' => \$opts{verbose},
'outdir:s' => \$opts_subcmd{outdir},
'prefix:s' => \$opts_subcmd{prefix},
'minDepth:s' => \$opts_subcmd{minDepth},
'maxDepth:s' => \$opts_subcmd{maxDepth},
'context:s' => \@{$opts_subcmd{context}}, # context
'flank:i' => \$opts_subcmd{flank},
'height:f' => \$opts_subcmd{height}, ## figure size: height
'width:f' => \$opts_subcmd{width}, ## figure size: width
'height2:f' => \$opts_subcmd{height2}, ## for histogram
'width2:f' => \$opts_subcmd{width2}, ## for histogram
'random_region:i' => \$opts_subcmd{random_region}, ## For heatmap error. annot allocate vector of size
'methodAverage' => \$opts_subcmd{methodAverage}, ## Calculate the average methylation level rather than the weighted methylated level.
},
subcommands => {
MethGeno => {
summary => 'Plot methylation information across the chromsome.',
# subcommand-specific options
options => {
# mandatory arguments
'genomeLength|g:s' => \$opts_subcmd{genomeLength},
'sample:s' => \@{$opts_subcmd{sample}},
# Optional arguments
'win:i' => \$opts_subcmd{win},
'step:i' => \$opts_subcmd{step},
'minLength:s' => \$opts_subcmd{minLength}, # cutoff for minimum length of chromosome.
'split:s' => \$opts_subcmd{'split'}, #
}
},
MethOverRegion => {
summary => 'Plot average distribution of methylation over your defined regions.',
options => {
# mandatory arguments
'region:s' => \$opts_subcmd{region},
'sample:s' => \@{$opts_subcmd{sample}},
# Optional arguments
'binLength:i' => \$opts_subcmd{binLength},
'binNumber:i' => \$opts_subcmd{binNumber},
'minLength:i' => \$opts_subcmd{minLength},
'maxLength:i' => \$opts_subcmd{maxLength},
'type:s' => \$opts_subcmd{type},
'regionName:s' => \$opts_subcmd{regionName},
#'legendTitle:s' => \$opts_subcmd{legendTitle},
}
},
MethHeatmap => {
summary => 'Generate heatmap for a given regions.',
options => {
# mandatory arguments
'regions:s' => \$opts_subcmd{region},
'sample:s' => \@{$opts_subcmd{sample}},
# Optional arguments
'merge' => \$opts_subcmd{merge}, ### if --merge is true, then methylation level of different will be generated in one file rather than one file for each context
'cluster_cols:s' => \$opts_subcmd{cluster_cols},
'cluster_rows:s' => \$opts_subcmd{cluster_rows},
}
},
MethOneRegion => {
summary => 'Generate heatmap for a given regions.',
options => {
'regions:s' => \$opts_subcmd{region},
'sample:s' => \@{$opts_subcmd{sample}},
}
},
MethCoverage => {
summary => 'Generate statistics of read coverage of the provided samples.',
options => {
'reference:s' => \$opts_subcmd{reference},
'sample:s' => \@{$opts_subcmd{sample}},
'outdir:s' => \$opts_subcmd{outdir},
}
},
MethLevDist => {
summary => 'Generate distribution of methylation levels for the provided samples.',
options => {
'sample:s' => \@{$opts_subcmd{sample}},
'regions:s' => \$opts_subcmd{region},
'binMethLev:s' => \$opts_subcmd{binMethLev},
}
},
GlobalMethLev => {
summary => 'Generate global (bulk) methylation levels for the provided samples.',
options => {
'sample:s' => \@{$opts_subcmd{sample}},
}
},
BisNonConvRate => {
summary => 'Estimate non-conversion rate of BS-seq data.',
options => {
'sample:s' => \@{$opts_subcmd{sample}},
'chrom:s' => \$opts_subcmd{chrom},
}
},
}
);
#print "UUXXX", join("\t", $resOpt->{subcommand}), "\n";
push @{$opts_subcmd{subcommand}}, @{$resOpt->{subcommand}} if exists $resOpt->{subcommand};
return $resOpt;
}
You can also get a copy of the file here: https://github.com/xie186/ViewBS/tree/66edfa79c35b404539ca3cdf4afcfd9c1bd20c6d/data/chk_issue25
