Error with "parse_entrez_gene_example.pl Sus_scrofa.ags"

[zoujing]

   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?
   

[zoujing]

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?
   

[Stefan Kirov-2]

AGS is a binary ASN.1 format and WILL NOT be parsed! You have to use
gene2xml( weird, but this is NCBI) with these flags: -c -x -b -i. This
will spit out text ASN which can be parsed.
Stefan

On Wed, 9 Apr 2008, 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?
>
> --
> View this message in context: http://www.nabble.com/Error-with-%22parse_entrez_gene_example.pl-Sus_scrofa.ags%22-tp16602770p16602770.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

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[Stefan Kirov-2]

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?
>>
>>
>
> --
> View this message in context: http://www.nabble.com/Error-with-%22parse_entrez_gene_example.pl-Sus_scrofa.ags%22-tp16602770p16603225.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@...
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>

_______________________________________________
Bioperl-l mailing list
Bioperl-l@...
http://lists.open-bio.org/mailman/listinfo/bioperl-l

[zoujing]

    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?
>>
>>
>
> --
> View this message in context: http://www.nabble.com/Error-with-%22parse_entrez_gene_example.pl-Sus_scrofa.ags%22-tp16602770p16603225.html
> Sent from the Perl - Bioperl-L mailing list archive at Nabble.com.
>
> _______________________________________________
> Bioperl-l mailing list
> [e-mail]
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
_______________________________________________
Bioperl-l mailing list
[e-mail]
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