[Bio] / FigKernelScripts / bielefeld_tarfile_to_seed.pl Repository:
ViewVC logotype

Diff of /FigKernelScripts/bielefeld_tarfile_to_seed.pl

Parent Directory Parent Directory | Revision Log Revision Log | View Patch Patch

revision 1.5, Fri Mar 31 21:00:21 2006 UTC revision 1.6, Wed Apr 12 19:49:11 2006 UTC
# Line 16  Line 16 
16  # http://www.theseed.org/LICENSE.TXT.  # http://www.theseed.org/LICENSE.TXT.
17  #  #
18    
   
19  use FIG;  use FIG;
20  $fig = new FIG;  $fig = new FIG;
21  # -*- perl -*-  
 s  
22  use File::Path;  use File::Path;
23    
24  $usage = "bielefeld_gff_to_seed.pl [-update] [-discard] input_tarfile output_dir";  $usage = "bielefeld_gff_to_seed.pl [-update] [-discard] input_tarfile output_dir";
# Line 85  Line 83 
83      print STDERR "Reading data from $tarfile\n";      print STDERR "Reading data from $tarfile\n";
84  }  }
85    
86    if ($tarfile =~ m/gz$/) {
87  &FIG::run("tar xpzvf $tarfile -C $dir");  &FIG::run("tar xpzvf $tarfile -C $dir");
88    } else {
89        &FIG::run("tar xpvf  $tarfile -C $dir");
90    }
91    
92  chdir("$base_dir/$output_dir") || "Could not change working-directory to $output_dir";  chdir("$base_dir/$output_dir") || "Could not change working-directory to $output_dir";
93  &FIG::run("cat RAW_DATA/*\.fas | reformat_contigs > contigs");  &FIG::run("cat RAW_DATA/*\.fas | reformat_contigs > contigs");

Legend:
Removed from v.1.5  
changed lines
  Added in v.1.6

MCS Webmaster
ViewVC Help
Powered by ViewVC 1.0.3