[Bioperl-l] Error with "parse_entrez_gene_example.pl Sus_scrofa.ags"

zoujing 1zoujing at 163.com
Thu Apr 10 03:10:26 EDT 2008


Seached  the web and found the answer now, quote the answer as following:
   The error was thrown by my Bio::ASN1::EntrezGene module because it 
expects a text file, while you fed it with a binary file.  To use 
gzipped ASN binary file from NCBI, download the NCBI gene2xml 
(ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/gene2xml), 
then use this syntax to run my parser on the binary files: 

my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i 
Homo_sapiens.ags.gz -c -x -b | "); # Homo_sapiens.ags.gz is the gzipped 
binary file directly downloaded from NCBI 

Same syntax should be used when you're using SeqIO (thus SeqIO::entrezgene). 
Mingyi

   But there is still one thing, I want to parse "gene_info.gz" in Gene of
NCBI. ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz.
   It doesn't work.Is that means "gene_info.gz"( tab-delimited,one line per
GeneID, Column header line is the first line in the file) is not the right
format for Bio::ASN1::EntrezGene?
 
      

zoujing wrote:
> 
>    I am a geen hand in Bioperl. When I run perl with
> "parse_entrez_gene_example.pl Sus_scrofa.ags", it turned out the error
> information:
>      Data Error: none conforming data found on line 1 in Sus_scrofa.ags.
>   
>    But the Sus_scrofa.ags is download from NCBI, with the format of ASN1,
> should be the same as Homo_sapiens in the example. So it should be no
> error as the code is the example from Mingyi.
>    I wonder why this happen, and should I change something about the file? 
>     
> 

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