Mercurial > repos > fcaramia > methylation_analysis_bismark
view methylation_analysis/methylation_extractor_wrapper.pl @ 5:23fed0cf09f4 draft
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author | fcaramia |
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date | Mon, 03 Dec 2012 18:27:11 -0500 |
parents | 282edadee017 |
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use strict; use warnings; use File::Basename; use Cwd; use File::Path qw(make_path remove_tree); die qq( Bad numbr of inputs ) if(!@ARGV); my @bam_list_entries; my $player_options = ""; my $bam_file; my $ending; my $genome; my $summary ; my $output; foreach my $input (@ARGV) { my @tmp = split "::", $input; if($tmp[0] eq "GENOME") { $genome=$tmp[1]; } elsif($tmp[0] eq "OPTION") { $player_options = "$player_options ${tmp[1]}"; } elsif($tmp[0] eq "ENDING") { $ending = $tmp[1]; } elsif($tmp[0] eq "BAMFILE") { $bam_file = $tmp[1]; } elsif($tmp[0] eq "SUMMARY") { $summary = $tmp[1]; } elsif($tmp[0] eq "OUTPUT") { $output = $tmp[1]; } else { die("Unknown Input: $input\n"); } } my $working_dir = cwd(); #convert bam to sam my $sam_file = "$working_dir/coverted.sam"; system("samtools view -h $bam_file > $sam_file"); #run bismark system ("bismark_methylation_extractor $ending $player_options --genome_folder $genome $sam_file > $summary 2>&1"); move_files($working_dir); sub move_files { my $name; my $suffix; my $path; my $local_dir = $_[0]; opendir(DIR, $local_dir); #print ("Openning: $local_dir\n"); my @FILES= readdir(DIR); closedir(DIR); foreach my $file (@FILES) { if ($file eq "." || $file eq "..") { #print ("./ or ../ skipped\n"); } elsif (-d "$local_dir/$file") { #print ("moving to: $local_dir/$file\n"); move_files("$local_dir/$file"); } elsif (-f "$local_dir/$file") { ($name,$path,$suffix) = fileparse($file,qr"\.[^.]*$"); if ($suffix eq ".bedGraph") { system ("mv $local_dir/$file $output"); } } else { die("Unrecognized file generated: $file\n"); } } }