[Bio] / FigMetagenomeTools / renumber_sequences.pl Repository:
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revision 1.2, Fri Mar 16 20:51:25 2007 UTC revision 1.3, Sat Apr 14 20:56:12 2007 UTC
# Line 38  Line 38 
38   elsif ($t eq "-p") {$asm_path = shift}   elsif ($t eq "-p") {$asm_path = shift}
39  }  }
40    
 $dbh->begin_work();  
   
41  unless ($qualf) {$qualf = $fastaf.".qual"}  unless ($qualf) {$qualf = $fastaf.".qual"}
42    
43  die $usage unless (-e $fastaf && -e $qualf);  die $usage unless (-e $fastaf && -e $qualf);
44  my ($count, $max);  my ($count, $max);
45    
46    $dbh->begin_work();
47    
48  if ($genomeno)  if ($genomeno)
49  {  {
50          $count=$genomeno;          $count=$genomeno;
# Line 111  Line 112 
112    
113      print "The new genome is number $count and the first sequence will be $max\nReading and dereplicating the fasta file\n";      print "The new genome is number $count and the first sequence will be $max\nReading and dereplicating the fasta file\n";
114  }  }
115    $dbh->commit();
116    
117  # read and de replicate the fasta file  # read and de replicate the fasta file
118  my $fasta=Rob->read_fasta($fastaf);  my $fasta=Rob->read_fasta($fastaf);
# Line 143  Line 145 
145          $max++;          $max++;
146  }  }
147    
 $dbh->commit();  

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