[Biophp-dev] hmmpfam parser

Thu, 12 Aug 2004 15:07:57 +0800

Yvan, many thanks for the contribution!!!  Better late than never, as they say.  

On my end, I've hit some sort of minor roadblock at the moment.  I'm looking for a good way to proceed.  Working with webservices, ontologies, visualization tools in Java (yeah, I have to) has taken away time from the BioPHP project, but has also given me a broader perspective on bioinformatics in general.  From time to time though, I manage to write PHP scripts in the course of my work.  A recent one is a parser for Ontology files in the OBO format (Open Biological Ontologies at http://sourceforge.net/projects/obo/).  I'll try and see if I can get my boss to agree to contribute the code to BioPHP.  

In the meantime, cheers to everyone...  

Regards,

Serge

----- Original Message -----
From: yvan <yvan.strahm@med.monash.edu.au>
Date: Thu, 12 Aug 2004 15:04:04 +1000
To: biophp-dev@bioinformatics.org
Subject: Re: [Biophp-dev] hmmpfam parser

> Hi guys,
> 
> Sorry for the delay.
> 
> Your parser is more finished then mine, furthermore my script use the  
> expat library which i guess make it more tricky to use. There is no  
> reason to depose it unless you want to have a look at. I am afraid now  
> it is more a script to parse a blast xml output and fill a database.  
> For the hmmpfam parser, it is very simple and a little buggy. It  only  
> parse file produced by hmmpfam, but you can have a look if you want. I  
> don't have time to make it PEARish. What it does. take a file  
> containing one or more hmmpfam outputs  and return a array of the kind:  
> array[sequence_name][domains][domains_data]. Being listed as a  
> developer, seems a little be to much as i don't know how much i could  
> contribute. So anyone who want the script let me know.
> 
> cheers
> yvan
> 
> On 27/07/2004, at 7:09 AM, S Clark wrote:
> 
> > Argh - sorry about the delay in posting - works insane right now...
> >
> > There actually is already a BLAST xml parser in CVS, though if yours
> > is better there's no reason we can't change over (for that matter
> > there's not really any reason we couldn't compare the two and combine  
> > them).
> >
> > If you want to have a look, you can see it in CVS at:
> >
> > https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi- 
> > official/ncbi_blast_parse_xml.inc.php
> > and the base xml parser from which this class is derived is at:
> > https://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/sean/semi- 
> > official/support_modules/parser_xml.inc.php
> >
> > Comments and suggestions welcome, as usual.  (I just noticed that  
> > although the
> > frontend class got copied over to the more official "genephp"  
> > subdirectory,
> > the parsers and NCBI-BLAST frontend didn't, apparently - will fix that
> > later...)
> >
> > Note that the "parsers" actually interpret the results and contain  
> > methods
> > for fetching the individual result fields as needed.  The whole result  
> > in
> > the form of an associative array (or "hash table" or whatever you want  
> > to call
> > it) is stored by the parser.
> >
> > If you want to contribute code, just let me know what your login is
> > at bioinformatics.org and I can add you to the developers list.
> >
> > Thanks!
> >
> > Sean
> >
> > On Friday 09 July 2004 10:42 am, Nico Stuurman wrote:
> >> Hi Yvan,
> >>
> >> You'll first need an account at bioinformatics.org and Sean has to add
> >> you as a developer.
> >>
> >> As for the code itself, we try to adhere the PEAR coding standards
> >> (http://pear.php.net/manual/en/standards.php).  Not all the code there
> >> has been PEARified yet, but you can look at biophp/genephp/seq.inc.php
> >> as an example.  Try to provide ample documentation and references to
> >> specific algorithms etc. if applicable.
> >>
> >> I am not sure where in the structure your parsers would fit (Sean, do
> >> you have a good idea about this?).  biophp/genephp/parsers is not a
> >> good idea since these are all parsers for sequence file formats (I
> >> guess we should rename parsers to importers).
> >> biophp/genephp/interfaces and biophp/genephp/utilities seem equally
> >> applicable right now.
> >>
> >> In the long run we should get some kind of datastructure holding  
> >> output
> >> from blast/fasta like services.  It would be great if you and Sean
> >> coudl think about that.
> >>
> >>
> >> Hope this helps,
> >>
> >>
> >> Nico
> >>
> >>> Just wondering what are the requirements for submiting codes to
> >>> Biophp? I wrote two parsers for hmmpfam and blast xml outputs, but am
> >>> afraid they are far from being useable in the context of biophp.
> >>>
> >>> Please, could someone explain me the DO and DONT?
> >>>
> >>> Regards
> >>>
> >>> Yvan
> >>>
> >>> _______________________________________________
> >>> Biophp-dev mailing list
> >>> Biophp-dev@bioinformatics.org
> >>> https://bioinformatics.org/mailman/listinfo/biophp-dev
> >>
> >> _______________________________________________
> >> Biophp-dev mailing list
> >> Biophp-dev@bioinformatics.org
> >> https://bioinformatics.org/mailman/listinfo/biophp-dev
> 
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