[Bio] / FigKernelScripts / promote_orfs_to_pegs.pl Repository:
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revision 1.6, Tue Nov 14 17:35:44 2006 UTC revision 1.7, Thu May 17 12:44:39 2007 UTC
# Line 47  Line 47 
47    
48  #...Build file of "nearby" PEGs  #...Build file of "nearby" PEGs
49  my $tmp_close = "$FIG_Config::temp/tmp_close_$$.fasta";  my $tmp_close = "$FIG_Config::temp/tmp_close_$$.fasta";
50  system("rm -f $tmp_close*");  system("/bin/rm -f $tmp_close*");
51  foreach $org (@neighbors) {  foreach $org (@neighbors) {
52      print STDERR "Appending $org to $tmp_close\n" if $ENV{VERBOSE};      print STDERR "Appending $org to $tmp_close\n" if $ENV{VERBOSE};
53      system("cat $FIG_Config::organisms/$org/Features/peg/fasta >> $tmp_close");      system("cat $FIG_Config::organisms/$org/Features/peg/fasta >> $tmp_close");
# Line 108  Line 108 
108      #      #
109      # Hrm, weird NFS effects here. There was a failure of this even though the directory      # Hrm, weird NFS effects here. There was a failure of this even though the directory
110      # was indeed empty.      # was indeed empty.
111      system("rm -fR $to_call_dir/Features/orf");      if (system("/bin/rm -fRv $to_call_dir/Features/orf")) {
     if (-d "$to_call_dir/Features/orf")  
     {  
112          warn "First remove did not work; sleeping and trying again";          warn "First remove did not work; sleeping and trying again";
113          sleep(2);          sleep(30);
114          system("rm -fR $to_call_dir/Features/orf");          system("/bin/rm -fRv $to_call_dir/Features/orf");
115      }      }
116  }  }
117  else {  else {

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