exception alphabet non reconnu
Bonjour à tous,
Je rencontre un probleme lorsque j'essaye de lire le fichier EMBL rel_con_env_01_r93.dat.gz après l'avoir decompressé.
voici le code :
Code:
1
2
3
4
5
6
7
|
my $dbin;
$dbin = Bio::SeqIO->new('-file' =>$infile, '-format' => $format, '-alphabet' => "dna") or die "Le fichier ne contien pas de sequence".$dbin->errstr;
print "alphabet ".$dbin->alphabet."\n";
my $seq;
$seq = $dbin->next_seq(); |
quand j'appelle next_seq() pour traiter les données il m'affiche l'erreur suivante:
Code:
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
|
-------------------- WARNING ---------------------
MSG: exception while parsing location line [join(AADL01000001.1:1..133665,gap(60),AADL01000002.1:1..784,gap(50),AADL01000003.1:1..1310,gap(50),AADL01000004.1:1..1019)] in reading EMBL/GenBank/SwissProt, ignoring feature CONTIG (seqid=unknown id):
------------- EXCEPTION -------------
MSG: operator "gap" unrecognized by parser
STACK Bio::Factory::FTLocationFactory::from_string /PERL/BioPerl_Modules//Bio/Factory/FTLocationFactory.pm:153
STACK Bio::Factory::FTLocationFactory::from_string /PERL/BioPerl_Modules//Bio/Factory/FTLocationFactory.pm:150
STACK (eval)
/PERL/BioPerl_Modules//Bio/SeqIO/FTHelper.pm:124
STACK Bio::SeqIO::FTHelper::_generic_seqfeature /PERL/BioPerl_Modules//Bio/SeqIO/FTHelper.pm:123
STACK Bio::SeqIO::embl::next_seq /PERL/BioPerl_Modules//Bio/SeqIO/embl.pm:342
STACK toplevel monfichier.pl:172
--------------------------------------
---------------------------------------------------
------------- EXCEPTION -------------
MSG: Got a sequence with no letters in - cannot guess alphabet []
STACK Bio::PrimarySeq::_guess_alphabet /PERL/BioPerl_Modules//Bio/PrimarySeq.pm:839
STACK Bio::PrimarySeq::seq
/PERL/BioPerl_Modules//Bio/PrimarySeq.pm:280
STACK Bio::PrimarySeq::new
/PERL/BioPerl_Modules//Bio/PrimarySeq.pm:217
STACK Bio::Seq::new
/PERL/BioPerl_Modules//Bio/Seq.pm:498
STACK Bio::Seq::RichSeq::new /PERL/BioPerl_Modules//Bio/Seq/RichSeq.pm:115
STACK Bio::Seq::SeqFactory::create /BioPerl_Modules//Bio/Seq/SeqFactory.pm:126
STACK Bio::SeqIO::embl::next_seq /PERL/BioPerl_Modules//Bio/SeqIO/embl.pm:364
STACK toplevel monfichier.pl:172 |
Si vous avez une idée pour ce probeleme je suis preneur.
merci
