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

zoujing 1zoujing at 163.com
Wed Apr 16 22:53:16 EDT 2008


    Thank you very much!
I splited the file on \t directly.

   Zou Jing


Stefan Kirov-2 wrote:
> 
> 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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