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

Stefan Kirov stefan.kirov at bms.com
Fri Apr 11 16:01:30 EDT 2008


It is not. If you use this file, why would you need a parser for it 
anyway? Just split on \t or read with OpenOffice or equiv.
Stefan

On Thu, 10 Apr 2008, zoujing wrote:

>
> 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 still one thing, I want to parse "gene_info.gz" in Gene of
> NCBI. 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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>
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