Mercurial > repos > fcaramia > contra
comparison contra_wrapper.pl @ 23:2770f49cb0dc
re-uploading contra
| author | Franco Caramia <franco.caramia@petermac.org> |
|---|---|
| date | Tue, 20 May 2014 09:59:00 +1000 |
| parents | |
| children | c361b3fb806e |
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| 22:e8a98923965e | 23:2770f49cb0dc |
|---|---|
| 1 use strict; | |
| 2 use warnings; | |
| 3 | |
| 4 use FindBin; | |
| 5 use File::Path qw(make_path); | |
| 6 use File::Spec; | |
| 7 | |
| 8 | |
| 9 die "Bad number of inputs" if(!@ARGV); | |
| 10 | |
| 11 my $player_options = ""; | |
| 12 my $contra_output; | |
| 13 my $contra_dir; | |
| 14 | |
| 15 | |
| 16 | |
| 17 foreach my $input (@ARGV) | |
| 18 { | |
| 19 my @tmp = split "::", $input; | |
| 20 | |
| 21 if($tmp[0] eq "PLAYEROPTION") | |
| 22 { | |
| 23 my $variable = $tmp[1]; | |
| 24 $variable =~ s/=/ /g; | |
| 25 print "$variable\n"; | |
| 26 $player_options = "$player_options $variable"; | |
| 27 } | |
| 28 elsif($tmp[0] eq "CONTRAOUTPUT") | |
| 29 { | |
| 30 $contra_output = $tmp[1]; | |
| 31 } | |
| 32 elsif($tmp[0] eq "CONTRADIR") | |
| 33 { | |
| 34 $contra_dir = $tmp[1]; | |
| 35 } | |
| 36 else | |
| 37 { | |
| 38 die("Unknown input: $input\n"); | |
| 39 } | |
| 40 } | |
| 41 | |
| 42 | |
| 43 my $working_dir = "CONTRA_OUTPUT"; | |
| 44 make_path($contra_dir); | |
| 45 #remove extension | |
| 46 | |
| 47 #run contra | |
| 48 system(File::Spec->catfile($FindBin::Bin, 'contra.py') . " -o $working_dir $player_options > /dev/null 2>&1"); | |
| 49 | |
| 50 #set html | |
| 51 #print "$contra_output - $working_dir\n"; | |
| 52 open(HTML, ">$contra_output"); | |
| 53 print HTML "<html><head><title>Contra: Copy Number Analysis for Targeted Resequencing</title></head><body><h3>Contra Output Files:</h3><p><ul>\n"; | |
| 54 move_files($working_dir); | |
| 55 print HTML "</ul></p>\n"; | |
| 56 close(HTML); | |
| 57 | |
| 58 sub move_files | |
| 59 { | |
| 60 my $local_dir = $_[0]; | |
| 61 opendir(DIR, $local_dir); | |
| 62 #print ("Openning: $local_dir\n"); | |
| 63 my @FILES= readdir(DIR); | |
| 64 closedir(DIR); | |
| 65 foreach my $file (@FILES) | |
| 66 { | |
| 67 if ($file eq "." || $file eq "..") | |
| 68 { | |
| 69 #print ("./ or ../ skipped\n"); | |
| 70 } | |
| 71 elsif (-d "$local_dir/$file") | |
| 72 { | |
| 73 #print ("moving to: $local_dir/$file\n"); | |
| 74 move_files("$local_dir/$file"); | |
| 75 } | |
| 76 elsif (-f "$local_dir/$file") | |
| 77 { | |
| 78 #print ("mv $local_dir/$file $contra_dir\n"); | |
| 79 print HTML "<li><a href=$file>$file</a></li>\n"; | |
| 80 system ("mv $local_dir/$file $contra_dir"); | |
| 81 } | |
| 82 else | |
| 83 { | |
| 84 die("Unrecognized file generated: $file\n"); | |
| 85 } | |
| 86 | |
| 87 | |
| 88 } | |
| 89 | |
| 90 } | |
| 91 |