Mercurial > repos > mini > strelka
view lib/Utils.pm @ 10:f66f23fcc83a
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author | mini |
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date | Tue, 30 Sep 2014 11:08:39 +0200 |
parents | 87568e5a7d4f |
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=head1 LICENSE Strelka Workflow Software Copyright (c) 2009-2013 Illumina, Inc. This software is provided under the terms and conditions of the Illumina Open Source Software License 1. You should have received a copy of the Illumina Open Source Software License 1 along with this program. If not, see <https://github.com/downloads/sequencing/licenses/>. =cut package Utils; use base 'Exporter'; our @EXPORT = qw( errorX logX executeCmd checkFile checkDir checkMove getAbsPath checkMakeDir getBinList parseConfigIni writeConfigIni ); use warnings FATAL => 'all'; use strict; use Carp; use Cwd qw(realpath); use File::Copy qw(move); use File::Path qw(mkpath); sub errorX($) { confess "\nERROR: " . $_[0] . "\n\n"; } sub logX($) { print STDERR "INFO: " . $_[0] . "\n"; } sub executeCmd($;$) { my $cmd = shift; my $isVerbose = shift; logX("Running: '$cmd'") if(defined($isVerbose) and $isVerbose); system($cmd) == 0 or errorX("Failed system call: '$cmd'"); } #return an error if file does not exist sub checkFile($;$) { my $file = shift; return if(-f $file); my $label = shift; errorX("Can't find" . (defined($label) ? " $label" : "") . " file: '$file'"); } #return an error if file does not Exist sub checkDir($;$) { my $dir = shift; return if(-d $dir); my $label = shift; errorX("Can't find" . (defined($label) ? " $label" : "") . " directory: '$dir'"); } sub checkMove($$) { my ($old,$new) = @_; move($old,$new) || errorX("File move failed: $!\n\tAttempting to move '$old' to '$new'"); } =item getAbsPath($path) This procedure attempts to convert a path provided by the user on the command line into an absolute path. It should be able to handle "~" paths and conventional relative paths using ".." or ".". Resolution of links should follow the convention of "Cwd::realpath". B<Parameters:> $dirRef - path (converted to absolute path in place) B<Returns:> returns zero if successful, non-zero otherwise. =cut sub getAbsPath(\$) { my ($dirRef) = @_; my @tmp=glob($$dirRef); return 1 if(scalar(@tmp) != 1); my $ret = Cwd::realpath($tmp[0]); return 1 if !$ret && !($ret = File::Spec->rel2abs($tmp[0])); $$dirRef = $ret; return 0; } #verify path is not a file, then create a directory with this name if does not exist sub checkMakeDir($) { my $dir = shift; unless (-e $dir) { File::Path::mkpath($dir) || errorX("Can't create directory '$dir'"); } else { errorX("Path is not a directory '$dir'\n") unless(-d $dir); } } sub getBinList($$) { my ($chromSize,$binSize) = @_; my $nm1 = (($chromSize-1) / $binSize); return [ map {sprintf("%04i",$_)} (0..$nm1) ]; } sub parseConfigError($$) { my ($file,$line) = @_; errorX("Config file '$file' contains unexpected line '$line'\n"); } #lis le fichier de config, si la ligne est de type : some space + [ some character ] + some space then register ther character in $section. ( [user] , then $section=user). sub parseConfigIni($) { my $file = shift; my %config; open(my $FH,"< $file") || errorX("Can't open config file '$file'"); my $section = "noSection"; while(<$FH>) { next if(/^[;#]/); next if(/^\s*$/); chomp; my $line=$_; my @ncl = split(/[;#]/); next unless(scalar(@ncl)); my $nc = $ncl[0]; if($nc =~ /^\s*\[([^\]]*)\]\s*$/) { $section = $1; next; } my ($key,$val) = map { s/^\s+//; s/\s+$//; $_ } split(/=/,$nc,2); unless(defined($key) && defined($val) && ($key ne "")) { parseConfigError($file,$line); } $config{$section}{$key} = $val; } close($FH); return \%config; } # minimal ini stringifier: # sub writeConfigIni($) { my $config = shift; my $val = ""; for my $section (sort(keys(%$config))) { $val .= "\n[$section]\n"; for my $key (sort(keys(%{$config->{$section}}))) { $val .= "$key = " . $config->{$section}{$key} . "\n"; } } return $val; } 1;