[Bioperl-l] Error with "parse_entrez_gene_example.pl Sus_scrofa.ags"
stefan.kirov at bms.com
Fri Apr 11 20:01:30 UTC 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.
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
> 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).
> 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
>> 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?
> View this message in context: http://www.nabble.com/Error-with-%22parse_entrez_gene_example.pl-Sus_scrofa.ags%22-tp16602770p16603225.html
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