[Bioperl-l] can't parse blast file anymore

[Hubert Prielinger]

Torsten Seemann wrote:
> Hubert
>
>> the following perl script worked fine until a few days ago....
>>
>>    #iterate over each query sequence
>>    print "try to enter while loop\n";
>>  
>>
> die "Bad BLAST report" if not defined $search;
>
>>    while (my $result = $search->next_result) {
>>    print "entered 1st while loop\n";
>>
>> Output:
>>
>> [Hubert at ppc7 Database_Search]$ /usr/bin/perl Blast.pl
>> try to enter while loop
>>
>> but it doesn't enter the first while loop, it stuck there, first I  
>>
> What is the value of $search before you start the WHILE loop ?
>
>


hi,
$search is defined, like

my $search = new Bio::SearchIO (-format => 'blast',
                                       -file => $file)


if I try it with the debugger as barry has suggested than I get the following

 

DB<1> n
main::(Blast.pl:24):    print "Connection established \n";
  DB<1> n
Connection established
main::(Blast.pl:26):    my $selectID = 0;
  DB<1> n
main::(Blast.pl:27):    my $count = 0;
  DB<1> n
main::(Blast.pl:37):    print "start program\n";
  DB<1> n
start program
main::(Blast.pl:38):    my $directory = '/home/Hubert/test';
  DB<1> n
main::(Blast.pl:39):    opendir(DIR, $directory) || die("Cannot open 
directory");
  DB<1> n
main::(Blast.pl:40):    print "opened directory\n";
  DB<1> n
opened directory
main::(Blast.pl:42):    foreach my $file (readdir(DIR))  {
  DB<1> n
main::(Blast.pl:43):      if ($file =~ /txt$/)   {
  DB<1> n
main::(Blast.pl:44):            $count++;
  DB<1> n
main::(Blast.pl:45):        print "read file $file \n";
  DB<1> n
read file 40026.txt
main::(Blast.pl:48):        $file = $directory . '/' . $file;
  DB<1> n
main::(Blast.pl:50):        my $search = new Bio::SearchIO (-format => 
'blast',
main::(Blast.pl:51):                                                           
-file => $file);
  DB<1> n
main::(Blast.pl:52):            print "bioperl seems to work....\n";
  DB<1> s $search
main::((eval 14)[/usr/lib/perl5/5.8.8/perl5db.pl:628]:3):
3:      $search;
  DB<<2>> n

  DB<2> n
bioperl seems to work....
main::(Blast.pl:53):        my $cutoff_len = 10;
  DB<2> n
main::(Blast.pl:56):        print "try to enter while loop\n";
  DB<2> n
try to enter while loop
main::(Blast.pl:57):        while (my $result = $search->next_result) {
  DB<2> s $result
main::((eval 15)[/usr/lib/perl5/5.8.8/perl5db.pl:628]:3):
3:      $result;
  DB<<3>>