Mercurial > repos > fcaramia > contra
comparison Contra/contra_wrapper.pl @ 0:7564f3b1e675
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| author | fcaramia |
|---|---|
| date | Thu, 13 Sep 2012 02:31:43 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:7564f3b1e675 |
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| 1 use strict; | |
| 2 use warnings; | |
| 3 use File::Basename; | |
| 4 use Cwd; | |
| 5 use File::Path qw(make_path remove_tree); | |
| 6 die qq( | |
| 7 Bad numbr of inputs | |
| 8 | |
| 9 ) if(!@ARGV); | |
| 10 | |
| 11 | |
| 12 my $player_options = ""; | |
| 13 my $contra_output; | |
| 14 my $contra_dir; | |
| 15 | |
| 16 my $dir = getcwd; | |
| 17 my $variable; | |
| 18 | |
| 19 foreach my $input (@ARGV) | |
| 20 { | |
| 21 my @tmp = split "::", $input; | |
| 22 | |
| 23 if($tmp[0] eq "PLAYEROPTION") | |
| 24 { | |
| 25 $variable = $tmp[1]; | |
| 26 $variable =~ s/=/ /g; | |
| 27 print "$variable\n"; | |
| 28 $player_options = "$player_options $variable"; | |
| 29 } | |
| 30 elsif($tmp[0] eq "CONTRAOUTPUT") | |
| 31 { | |
| 32 $contra_output = $tmp[1]; | |
| 33 } | |
| 34 elsif($tmp[0] eq "CONTRADIR") | |
| 35 { | |
| 36 $contra_dir = $tmp[1]; | |
| 37 } | |
| 38 else | |
| 39 { | |
| 40 die("Unknown Input: $input\n"); | |
| 41 } | |
| 42 } | |
| 43 | |
| 44 | |
| 45 my $working_dir = "CONTRA_OUTPUT"; | |
| 46 make_path($contra_dir); | |
| 47 #remove extension | |
| 48 | |
| 49 #run contra | |
| 50 system ("contra.py -o $working_dir $player_options > /dev/null 2>&1"); | |
| 51 | |
| 52 | |
| 53 #set html | |
| 54 #print "$contra_output - $working_dir\n"; | |
| 55 open(HTML, ">$contra_output"); | |
| 56 print HTML "<html><head><title>Contra: Copy Number Analysis for Targeted Resequencing</title></head><body><h3>Contra Output Files:</h3><p><ul>\n"; | |
| 57 move_files($working_dir); | |
| 58 print HTML "</ul></p>\n"; | |
| 59 close(HTML); | |
| 60 | |
| 61 sub move_files | |
| 62 { | |
| 63 my $local_dir = $_[0]; | |
| 64 opendir(DIR, $local_dir); | |
| 65 #print ("Openning: $local_dir\n"); | |
| 66 my @FILES= readdir(DIR); | |
| 67 closedir(DIR); | |
| 68 foreach my $file (@FILES) | |
| 69 { | |
| 70 if ($file eq "." || $file eq "..") | |
| 71 { | |
| 72 #print ("./ or ../ skipped\n"); | |
| 73 } | |
| 74 elsif (-d "$local_dir/$file") | |
| 75 { | |
| 76 #print ("moving to: $local_dir/$file\n"); | |
| 77 move_files("$local_dir/$file"); | |
| 78 } | |
| 79 elsif (-f "$local_dir/$file") | |
| 80 { | |
| 81 #print ("mv $local_dir/$file $contra_dir\n"); | |
| 82 print HTML "<li><a href=$file>$file</a></li>\n"; | |
| 83 system ("mv $local_dir/$file $contra_dir"); | |
| 84 } | |
| 85 else | |
| 86 { | |
| 87 die("Unrecognized file generated: $file\n"); | |
| 88 } | |
| 89 | |
| 90 | |
| 91 } | |
| 92 | |
| 93 } | |
| 94 |