[Bioperl-l] Problem with genbank.pm ?

[Alberto Davila]

Dear All,

Trying to run the script below I got several errors and a "segmentation
fault" ...

I was trying to get the Xylella fasitidiosa genome from the "genome"
subset of genbank then put it in a MySQL (MyISAM) table containing a
column formatted as "mediumblob/binary"...

Any tips to solve this ?

Thanks, Alberto

******

#!/usr/local/bin/perl -w
 
 
use lib "/usr/local/bioperl14";
use Bio::SearchIO;
use Bio::DB::Query::GenBank;
use Bio::SeqIO;
use Bio::DB::GenBank;
 

my $organismname = $ARGV[0];
my $Lib_Code = $ARGV[1];
 
%Lib = (1,"GIG",2,"EST",3,GSS,4,STS,5,"Genome");
                                                                                
my $genbankfile = "GenBank."."$organismname."."$Lib{$Lib_Code}";
 
 
&download ($organismname,$Lib_Code);
&submit_download ($genbankfile,$Lib_Code);
 
 
sub download {
 
 
#Menu: 1 - Genes in genomic; 2 - EST; 3 - GSS; 4 - STS; 5 - Genome; 6 -
Local
  
#my $query_string2;
 
if ($Lib_Code =~ /1/) {
        $query_string = $organismname."[Organism] AND \"genes in
genomic\"[Properties]";
}
elsif ($Lib_Code =~ /2/) {
        $query_string = $organismname."[Organism] AND \"gbdiv
est\"[Properties]";
}
elsif ($Lib_Code =~ /3/) {
        $query_string = $organismname."[Organism] AND \"gbdiv
gss\"[Properties]";
}
elsif ($Lib_Code =~ /4/) {
        $query_string = $organismname."[Organism] AND \"gbdiv
sts\"[Properties]";
}
elsif ($Lib_Code =~ /5/) {
        $query_string2 = $organismname."[Organism]";
}
 
 
 
if ($Lib_Code < 5) {
 
$query = new Bio::DB::Query::GenBank(-db=>'nucleotide',
                                        -query=>$query_string,
                                        -mindate => '1985',
                                        -maxdate => '2004');
$count = $query->count;
                                                                                
$seqio=new Bio::DB::GenBank->get_Stream_by_query($query);
 
 
} elsif ($Lib_Code == 5) {
 
$query2 = new Bio::DB::Query::GenBank(-db=>'genome',
                                        -query=>$query_string2,
                                        -mindate => '1985',
                                        -maxdate => '2004');
$count = $query2->count;
$seqio=new Bio::DB::GenBank->get_Stream_by_query($query2);
}
 

ERROR LOG:

Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189592.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189593.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189595.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189596.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189598.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189599.
                                                                                
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189600.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189601.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189603.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189605.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189607.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189609.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189610.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189612.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189614.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189616.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189618.
                                                                                
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189620.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189622.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189624.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189630.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in concatenation (.) or string at
/usr/local/bioperl14/Bio/SeqIO/genbank.pm line 492,
<STREAM> line 189631.
  
-------------------- WARNING ---------------------
MSG: Unexpected error in feature table for  Skipping feature, attempting
to recover
---------------------------------------------------
Use of uninitialized value in length at
/usr/local/bioperl14/Bio/SeqIO/fasta.pm
line 205, <STREAM> line 189631.
8
Segmentation fault