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