[Biojava-dev] Biojava - svn migration was : bioperl like blastparser
Hilmar Lapp
hlapp at duke.edu
Wed Dec 26 23:41:54 UTC 2007
On Dec 26, 2007, at 6:29 PM, Andreas Prlic wrote:
>
>> You just need to put the repositor(ies) in
>> /home/svn-repositories/biojava
>
> Thanks for the info. I now have the new biojava svn repository for
> developers running
Great, congrats!
> and it is possible to check out (and do commits) via
>
> svn co svn+ssh://dev.open-bio.org/home/svn-repositories/biojava/
> biojava-svn/biojava-live/trunk/ ./biojava-svn
Is this the directory structure template we should all mirror for the
different projects? I suppose some consistency isn't bad ...
The URL looks awfully long - did we choose not to use /home/svn
(instead of /home/svn-repositories), and is the intervening 'biojava-
svn directory needed?
I.e., is root URL of the repository at /home/svn-repositories/biojava/
biojava-svn/biojava-live/, or /home/svn-repositories/biojava/ ?
-hilmar
>
> I am just running final tests to see if all is fine. Access should
> work for other biojava developers as well.
>
>
> For the anonymous access - who will set this up? I assume there
> will be a commit hook in the developers repository which will do a
> svnsync with the anonymous repository?
>
> Andreas
>
>
>
>
>
>>
>> anyone in the biojava group can write there.
>> you'll want to delete the existing biojava-live that is in there.
>>
>> I'm traveling most of 26th and will be on vacation most of the
>> week, but will check in when I have a chance.
>>
>> -jason
>>
>> On Dec 25, 2007, at 3:42 PM, Andreas Prlic wrote:
>>
>>> Hi Mark,
>>>
>>> Unfortunately the biojava svn respository is not ready yet.
>>>
>>> George has converted our CVS to an initial svn dump, which I
>>> tested and fixed some details.
>>> This dump has been ready since dezember 17th. - ( see dev.open-
>>> bio.org:~andreas/biojava-final.svndump.bz2 )
>>> The next step is to load this into the public open-bio
>>> repository, after which (and some more testing) the new biojava
>>> repository would be ready for new commits.
>>>
>>> At the present I am waiting for somebody who has admin rights on
>>> the open-bio servers to do these final steps.
>>> (or to delegate and give permissions to somebody else).
>>>
>>> I tried to contact support at open-bio, root-l, as well as mailing
>>> several people directly,
>>> but so far I did not get a response. could be that the holiday
>>> season is slowing response times down...
>>>
>>> Andreas
>>>
>>>
>>>
>>> On 25 Dec 2007, at 21:44, Mark Schreiber wrote:
>>>
>>>> Hi -
>>>>
>>>> When will the subversion system be ready for checkin?
>>>>
>>>> - Mark
>>>>
>>>> On Dec 24, 2007 4:29 PM, Michael Gang <michaelgang at gmail.com>
>>>> wrote:
>>>>> OK,
>>>>> I made four changes,
>>>>> in the package org.biojava.bio.program.sax; at class
>>>>> BlastSaxParser
>>>>> 1) at line 86 i added the variable
>>>>> private String
>>>>> oQueryLength;
>>>>> 2) at the method private void interpret(String poLine) throws
>>>>> SAXException
>>>>> in the if "if (iState == IN_HEADER) {"
>>>>> at line 209 i added
>>>>>
>>>>> if (poLine.startsWith("(", 9) && poLine.endsWith("letters)") ) {
>>>>> StringTokenizer st = new StringTokenizer(poLine);
>>>>> oQueryLength = st.nextToken().substring(1);
>>>>> }
>>>>> 3)at the function private void emitHeaderIds() throws
>>>>> SAXException {
>>>>> at line 564 i added
>>>>> oAttQName.setQName("queryLength");
>>>>> oAtts.addAttribute(oAttQName.getURI(),
>>>>> oAttQName.getLocalName(),
>>>>> oAttQName.getQName(),
>>>>> "CDATA", oQueryLength);
>>>>>
>>>>> at the package org.biojava.bio.program.ssbind; in
>>>>> HeaderStAXHandler.java
>>>>> 4)at the private class QueryIDStAXHandler at line 95 I changed the
>>>>> method startelement
>>>>>
>>>>> public void startElement(String uri,
>>>>> String localName,
>>>>> String qName,
>>>>> Attributes attr,
>>>>> DelegationManager dm)
>>>>> throws SAXException
>>>>> {
>>>>> ssContext.getSearchContentHandler().setQueryID
>>>>> (attr.getValue("id"));
>>>>> if (attr.getValue("queryLength") != null)
>>>>> {
>>>>> ssContext.getSearchContentHandler
>>>>> ().addSearchProperty("queryLength",
>>>>> attr.getValue("queryLength"));
>>>>> }
>>>>> }
>>>>> }
>>>>>
>>>>> Now query length is a property of the annotation of a blast
>>>>> result.
>>>>> It is really fun to participate in the biojava project.
>>>>>
>>>>> Best regards,
>>>>> Michael
>>>>>
>>>>>
>>>>> On Dec 24, 2007 2:32 AM, Mark Schreiber
>>>>> <markjschreiber at gmail.com> wrote:
>>>>>> Hi -
>>>>>>
>>>>>> We are currently merging the code base into subversion (from CVS)
>>>>>> after this it will be possible to check in code again. For small
>>>>>> additions it is usually easier to post the code to the dev
>>>>>> list (in
>>>>>> the body of the email as the list doesn't like attachments) or
>>>>>> send it
>>>>>> to one of the regular committers and get them to add it.
>>>>>>
>>>>>> The JUnit tests are the standard test package. If you have
>>>>>> added new
>>>>>> functionality it would be a good idea to add another test
>>>>>> method in
>>>>>> the appropriate JUnit test to make sure it works (and
>>>>>> continues to
>>>>>> work in the future).
>>>>>>
>>>>>> - Mark
>>>>>>
>>>>>>
>>>>>> On Dec 23, 2007 11:22 PM, Michael Gang <michaelgang at gmail.com>
>>>>>> wrote:
>>>>>>> Hi all,
>>>>>>>
>>>>>>> I've now added the extraction of the query length.
>>>>>>> Can someone explain me the procedure of checking in code to
>>>>>>> biojava ?
>>>>>>> I ran the unit tests in the biojava distribution? Are there
>>>>>>> additional
>>>>>>> tests available ?
>>>>>>>
>>>>>>> Best regards,
>>>>>>> Michael
>>>>>>>
>>>>>>>
>>>>>>> On Dec 21, 2007 9:59 AM, Mark Schreiber
>>>>>>> <markjschreiber at gmail.com> wrote:
>>>>>>>> Hi -
>>>>>>>>
>>>>>>>> It is not required that you turn all Blast results into
>>>>>>>> objects,
>>>>>>>> because it is an event based parser you can do what you want
>>>>>>>> with the
>>>>>>>> events including turning them into objects or echoing them
>>>>>>>> to STDOUT.
>>>>>>>> Take a look at the examples in the cookbook.
>>>>>>>>
>>>>>>>> It may be that the query length is actually parsed but is
>>>>>>>> not passed
>>>>>>>> onto the object model by the event listeners.
>>>>>>>>
>>>>>>>> - Mark
>>>>>>>>
>>>>>>>>
>>>>>>>> On Dec 21, 2007 12:15 AM, Andreas Prlic <ap3 at sanger.ac.uk>
>>>>>>>> wrote:
>>>>>>>>> Hi Michael,
>>>>>>>>>
>>>>>>>>> The blast parser (BlastLikeSaxParser) in BioJava has been
>>>>>>>>> around for
>>>>>>>>> a while and is frequently being used to parse a variety
>>>>>>>>> of different blast outputs. Still it is not complete and
>>>>>>>>> can not
>>>>>>>>> parse PSI blast. We have had a number of request about it
>>>>>>>>> lately
>>>>>>>>> so I suppose it needs a little maintenance now.
>>>>>>>>>
>>>>>>>>> To write a new blast parser from scratch will involve a
>>>>>>>>> significant
>>>>>>>>> amount of time. It will take time to fix all the bugs, add
>>>>>>>>> support
>>>>>>>>> for the different blast versions and write documentation.
>>>>>>>>> Much of
>>>>>>>>> this is already available in BioJava, so I would prefer if
>>>>>>>>> you could
>>>>>>>>> submit patches for
>>>>>>>>> the current blast parser. Would you also be interested to
>>>>>>>>> collaborate in this direction?
>>>>>>>>> Another feature that would be nice to add support for is the
>>>>>>>>> possibility to send off blast searches to webservices...
>>>>>>>>>
>>>>>>>>> Cheers,
>>>>>>>>> Andreas
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> On 20 Dec 2007, at 12:54, Michael Gang wrote:
>>>>>>>>>
>>>>>>>>>> Hi All,
>>>>>>>>>>
>>>>>>>>>> I used the interface of the java blast parser.
>>>>>>>>>> I had mainly two problems with it:
>>>>>>>>>> 1) The blast parser does not parse all the information
>>>>>>>>>> (for example
>>>>>>>>>> query length)
>>>>>>>>>> 2) The blast parser parses the whole blast report into a
>>>>>>>>>> list which
>>>>>>>>>> eats a lot of memory.
>>>>>>>>>>
>>>>>>>>>> I would be interested to write and contribute a blast
>>>>>>>>>> parser which
>>>>>>>>>> parses all the information of the blast and parses the blast
>>>>>>>>>> iteratively.
>>>>>>>>>> Something like the following code in bioperl (just in Java).
>>>>>>>>>> use Bio::SearchIO;
>>>>>>>>>> # format can be 'fasta', 'blast'
>>>>>>>>>> my $searchio = new Bio::SearchIO( -format => 'blastxml',
>>>>>>>>>> -file =>
>>>>>>>>>> 'blastout.xml' );
>>>>>>>>>> while ( my $result = $searchio->next_result() ) {
>>>>>>>>>> while( my $hit = $result->next_hit ) {
>>>>>>>>>> # process the Bio::Search::Hit::HitI object
>>>>>>>>>> while( my $hsp = $hit->next_hsp ) {
>>>>>>>>>> # process the Bio::Search::HSP::HSPI object
>>>>>>>>>> }
>>>>>>>>>> }
>>>>>>>>>>
>>>>>>>>>> Would you be interested in such a contribution ?
>>>>>>>>>>
>>>>>>>>>> Best regards,
>>>>>>>>>> Michael
>>>>>>>>>> _______________________________________________
>>>>>>>>>> biojava-dev mailing list
>>>>>>>>>> biojava-dev at lists.open-bio.org
>>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>>>>>>
>>>>>>>>> --------------------------------------------------------------
>>>>>>>>> ---------
>>>>>>>>>
>>>>>>>>> Andreas Prlic Wellcome Trust Sanger Institute
>>>>>>>>> Hinxton, Cambridge CB10 1SA, UK
>>>>>>>>> +44 (0) 1223 49 6891
>>>>>>>>>
>>>>>>>>> --------------------------------------------------------------
>>>>>>>>> ---------
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> The Wellcome Trust Sanger Institute is operated by Genome
>>>>>>>>> Research
>>>>>>>>> Limited, a charity registered in England with number
>>>>>>>>> 1021457 and a
>>>>>>>>> company registered in England with number 2742969, whose
>>>>>>>>> registered
>>>>>>>>> office is 215 Euston Road, London, NW1 2BE.
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> biojava-dev mailing list
>>>>>>>>> biojava-dev at lists.open-bio.org
>>>>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>>>>>>
>>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> biojava-dev mailing list
>>>>>>> biojava-dev at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>>>>
>>>>>>
>>>>> _______________________________________________
>>>>> biojava-dev mailing list
>>>>> biojava-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>>>
>>>> _______________________________________________
>>>> biojava-dev mailing list
>>>> biojava-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/biojava-dev
>>>
>>> --------------------------------------------------------------------
>>> ---
>>>
>>> Andreas Prlic Wellcome Trust Sanger Institute
>>> Hinxton, Cambridge CB10 1SA, UK
>>> +44 (0) 1223 49 6891
>>>
>>> --------------------------------------------------------------------
>>> ---
>>>
>>>
>>>
>>>
>>> --
>>> The Wellcome Trust Sanger Institute is operated by Genome
>>> ResearchLimited, a charity registered in England with number
>>> 1021457 and acompany registered in England with number 2742969,
>>> whose registeredoffice is 215 Euston Road, London, NW1 2BE.
>>
>
> ----------------------------------------------------------------------
> -
>
> Andreas Prlic Wellcome Trust Sanger Institute
> Hinxton, Cambridge CB10 1SA, UK
> +44 (0) 1223 49 6891
>
> ----------------------------------------------------------------------
> -
>
>
>
>
> --
> The Wellcome Trust Sanger Institute is operated by Genome
> ResearchLimited, a charity registered in England with number
> 1021457 and acompany registered in England with number 2742969,
> whose registeredoffice is 215 Euston Road, London, NW1 2BE.
--
===========================================================
: Hilmar Lapp -:- Durham, NC -:- hlapp at duke dot edu :
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