NCBI xml parser

[Pierre-Yves-3]

Dear list,

I am trying to find my way around parsing ncbi blast xml.
I am using a small library which performs the blast online [1] and
returns a FileReader of the xml.
I can convert the FileReader to a string and print it, it seems fine.
(I used the default input shown on [1]).

So I am now trying to parse it automatically. I looked at [2] and [3]
but I could not get them working. I then found this message from this
mailing list [4] and thus went to use BlastXMLParserFacade.
It returns me an "org.xml.sax.SAXException: illegal frame number
encountered. (0)".

So my question is then: which method should I use ?

Thanks in advance,

Best regards,

Pierre



[1] http://users.encs.concordia.ca/~f_kohant/ncbiblast/
[2] http://biojava.org/wiki/BioJava:CookBook:Blast:Echo
[3]
http://biojava.org/wiki/BioJava:Tutorial:Blast-like_Parsing_Cook_Book
[4] http://osdir.com/ml/java.bio.general/2005-06/msg00018.html



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[Josh Goodman]

It looks like the new BLAST+ binary is using a default frame of 0 instead of the old default of 1
for blastp.  Hence the illegal frame number (0) error.

Josh

Pierre-Yves wrote:

> Dear list,
>
> I am trying to find my way around parsing ncbi blast xml.
> I am using a small library which performs the blast online [1] and
> returns a FileReader of the xml.
> I can convert the FileReader to a string and print it, it seems fine.
> (I used the default input shown on [1]).
>
> So I am now trying to parse it automatically. I looked at [2] and [3]
> but I could not get them working. I then found this message from this
> mailing list [4] and thus went to use BlastXMLParserFacade.
> It returns me an "org.xml.sax.SAXException: illegal frame number
> encountered. (0)".
>
> So my question is then: which method should I use ?
>
> Thanks in advance,
>
> Best regards,
>
> Pierre
>
>
>
> [1] http://users.encs.concordia.ca/~f_kohant/ncbiblast/
> [2] http://biojava.org/wiki/BioJava:CookBook:Blast:Echo
> [3]
> http://biojava.org/wiki/BioJava:Tutorial:Blast-like_Parsing_Cook_Book
> [4] http://osdir.com/ml/java.bio.general/2005-06/msg00018.html
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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[Pierre-Yves-3]

On Mon, 2009-11-02 at 09:45 -0500, Josh Goodman wrote:
> It looks like the new BLAST+ binary is using a default frame of 0 instead of the old default of 1
> for blastp.  Hence the illegal frame number (0) error.
>
> Josh

Thanks for the hint.

I downloaded the biojava-1.7-src.jar to check the sources and correct
the frame to 0 (I already saw the case to change).
However, without changing anything on the source, when I try to
reproduce the error, I got a new one:
"org.xml.sax.SAXParseException: The markup declarations contained or
pointed to by the document type declaration must be well-formed."

I understand the error, I am more surprised by the fact that the jar
and the sources of the release 1.7 are given a different errors.

Did I miss something ?

Thanks,
Best regards,

Pierre

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[Andreas Prlic-3]

>
>
> I understand the error, I am more surprised by the fact that the jar
> and the sources of the release 1.7 are given a different errors.
>
>
that's surprising... I built the src-jar and the other jars at the same time
so the code should be identical... Are you sure you are doing exactly the
same?

Andreas
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[Pierre-Yves-3]

On 11/02/2009 08:29 PM, Andreas Prlic wrote:
>>
>> I understand the error, I am more surprised by the fact that the jar
>> and the sources of the release 1.7 are given a different errors.
>>
>>
> that's surprising... I built the src-jar and the other jars at the same time
> so the code should be identical... Are you sure you are doing exactly the
> same?

I can confirm you this tomorrow but AFAIR before I left I tried the same
code using or the jar file or the project generated from the sources in
NetBeans and it gaves me two differents errors.

Best regards,
Pierre
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[Pierre-Yves-3]

On Mon, 2009-11-02 at 20:50 +0100, Pierre-Yves wrote:

> On 11/02/2009 08:29 PM, Andreas Prlic wrote:
> >>
> >> I understand the error, I am more surprised by the fact that the jar
> >> and the sources of the release 1.7 are given a different errors.
> >>
> >>
> > that's surprising... I built the src-jar and the other jars at the same time
> > so the code should be identical... Are you sure you are doing exactly the
> > same?
>
> I can confirm you this tomorrow but AFAIR before I left I tried the same
> code using or the jar file or the project generated from the sources in
> NetBeans and it gaves me two differents errors.

Ok so just for the record:
- If I use the .jar file I get an error (1)
- If I create a project in NetBeans using the source from BioJava I get
a different error (2)
- If I add as dependencies the sources from BioJava I get the first
error (1)

I thus went for the third solution and found my way around :-)

Thanks for the help.

Best regards,

Pierre

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[Andreas Prlic-2]

So what you are saying is that you had a classpath problem and by  
configuring dependencies correctly the problem went away?
Andreas

On 3 Nov 2009, at 06:45, Pierre-Yves <pingou@...> wrote:

> On Mon, 2009-11-02 at 20:50 +0100, Pierre-Yves wrote:
>> On 11/02/2009 08:29 PM, Andreas Prlic wrote:
>>>>
>>>> I understand the error, I am more surprised by the fact that the  
>>>> jar
>>>> and the sources of the release 1.7 are given a different errors.
>>>>
>>>>
>>> that's surprising... I built the src-jar and the other jars at the  
>>> same time
>>> so the code should be identical... Are you sure you are doing  
>>> exactly the
>>> same?
>>
>> I can confirm you this tomorrow but AFAIR before I left I tried the  
>> same
>> code using or the jar file or the project generated from the  
>> sources in
>> NetBeans and it gaves me two differents errors.
>
> Ok so just for the record:
> - If I use the .jar file I get an error (1)
> - If I create a project in NetBeans using the source from BioJava I  
> get
> a different error (2)
> - If I add as dependencies the sources from BioJava I get the first
> error (1)
>
> I thus went for the third solution and found my way around :-)
>
> Thanks for the help.
>
> Best regards,
>
> Pierre
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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[Pierre-Yves-3]

On Tue, 2009-11-03 at 06:56 -0800, Andreas Prlic wrote:
> So what you are saying is that you had a classpath problem and by  
> configuring dependencies correctly the problem went away?

In both case it was compiling, only the error at run time was different.

Regards,

Pierre

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[Andreas Prlic-2]

Can you send me the code snipplet off list so I can take a look? Thanks,
A

On 3 Nov 2009, at 07:00, Pierre-Yves <pingou@...> wrote:

> On Tue, 2009-11-03 at 06:56 -0800, Andreas Prlic wrote:
>> So what you are saying is that you had a classpath problem and by
>> configuring dependencies correctly the problem went away?
>
> In both case it was compiling, only the error at run time was  
> different.
>
> Regards,
>
> Pierre
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l

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[jitesh dundas]

Dear Sir,

I am not using any of those methods. However, I have written a code to parse
through an XML file for pubmed data.

Hope this might help you.

Regards,
Jitesh Dundas

On Mon, Nov 2, 2009 at 7:33 PM, Pierre-Yves <pingou@...> wrote:

> Dear list,
>
> I am trying to find my way around parsing ncbi blast xml.
> I am using a small library which performs the blast online [1] and
> returns a FileReader of the xml.
> I can convert the FileReader to a string and print it, it seems fine.
> (I used the default input shown on [1]).
>
> So I am now trying to parse it automatically. I looked at [2] and [3]
> but I could not get them working. I then found this message from this
> mailing list [4] and thus went to use BlastXMLParserFacade.
> It returns me an "org.xml.sax.SAXException: illegal frame number
> encountered. (0)".
>
> So my question is then: which method should I use ?
>
> Thanks in advance,
>
> Best regards,
>
> Pierre
>
>
>
> [1] http://users.encs.concordia.ca/~f_kohant/ncbiblast/<http://users.encs.concordia.ca/%7Ef_kohant/ncbiblast/>
> [2] http://biojava.org/wiki/BioJava:CookBook:Blast:Echo
> [3]
> http://biojava.org/wiki/BioJava:Tutorial:Blast-like_Parsing_Cook_Book
> [4] http://osdir.com/ml/java.bio.general/2005-06/msg00018.html
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@...
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>

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