From biophp-dev@bioinformatics.org Thu Jul 1 08:30:36 2004
From: biophp-dev@bioinformatics.org (biophp-dev@bioinformatics.org)
Date: Thu, 1 Jul 2004 09:30:36 +0200
Subject: [Biophp-dev] Question
Message-ID: <53D963F97CB58646886BEAFC25E0FAFB02FC9B@crbsmxsusr02.pharma.aventis.com>
Question
Hello ,
I was busy during =
the last months so my Locuslink file is still under construction, by the =
way, what is the way if I want to append my code to this directory =
:
http://bioi=
nformatics.org/cgi-bin/cvsweb.cgi/biophp/
My question is : =
Does any one have a biophp module to automatically convert a fasta file =
into an embl or genbank file. Actually I use Bioperl to do that but I =
would be glad to do all in PHP. If it doesn't exist a solution yet I =
will try to take the time to build it. Ha It would be great if the days =
were 24 hours longer !!!!!!!
Thanks in advance =
Fred
From biophp-dev@bioinformatics.org Thu Jul 1 17:51:20 2004
From: biophp-dev@bioinformatics.org (S Clark)
Date: Thu, 1 Jul 2004 10:51:20 -0600
Subject: [Biophp-dev] Question
In-Reply-To: <53D963F97CB58646886BEAFC25E0FAFB02FC9B@crbsmxsusr02.pharma.aventis.com>
References: <53D963F97CB58646886BEAFC25E0FAFB02FC9B@crbsmxsusr02.pharma.aventis.com>
Message-ID: <200407011051.25971.mail-lists+biophpdev@dogphilosophy.net>
In order to add code to the CVS tree at bioinformatics.org, you'll need
a bioinformatics.org login name, and I'll need to add it to the
developers list...and that's about it. (The instructions for CVS itself
are on the bioinformatics.org website). If you already have a
bioinformatics.org login (or as soon as you've got one) let me know and
I'll add you to the developer list.
We DO have import and export frameworks ready for initial use, but the
only export module currently written is a simple FASTA example. If you
had time to add a Genbank and/or embl format module in the same style to
add to the export section that'd be very helpful! Take a look at
seqIOExport.inc.php and exporters/export_fasta.inc.php - that should
(hopefully) show how an "export_genbank.inc.php" class should be
structured (comments and suggestions, as always, are welcome...)
The current code is (for the moment) actually residing in the "genephp"
section. Reorganization under the biophp section should happen Real Soon Now.
(The whole "two different-but-cross-pollinating projects with the same name"
thing IS a bit confusing...)
We may be really quiet right now (probably a combination of work and school
hitting us all again - that's MY excuse, anyway) but we're not dead yet...
Thanks!
Sean
P.S. I'm not sure about getting 24 extra hours in the day - I have a sneaking
suspicion that the work day would just expand to compensate.
That kilo of that pure laboratory-grade Caffeine in the chemical supply
catalogs looks more appealing all the time...
On Thursday 01 July 2004 01:30 am, Frederic.Fleche@aventis.com wrote:
> Hello ,
> I was busy during the last months so my Locuslink file is still under
> construction, by the way, what is the way if I want to append my code to
> this directory :
>
>
> http://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/
> My question is : Does any one have a biophp module to automatically convert
> a fasta file into an embl or genbank file. Actually I use Bioperl to do
> that but I would be glad to do all in PHP. If it doesn't exist a solution
> yet I will try to take the time to build it. Ha It would be great if the
> days were 24 hours longer !!!!!!!
>
>
> Thanks in advance
> Fred
From biophp-dev@bioinformatics.org Fri Jul 2 01:16:06 2004
From: biophp-dev@bioinformatics.org (Nico Stuurman)
Date: Thu, 1 Jul 2004 17:16:06 -0700
Subject: [Biophp-dev] Question
In-Reply-To: <200407011051.25971.mail-lists+biophpdev@dogphilosophy.net>
References: <53D963F97CB58646886BEAFC25E0FAFB02FC9B@crbsmxsusr02.pharma.aventis.com> <200407011051.25971.mail-lists+biophpdev@dogphilosophy.net>
Message-ID: <02A8F43F-CBBD-11D8-97C2-00039353BA82@itsa.ucsf.edu>
>
> We may be really quiet right now (probably a combination of work and
> school
> hitting us all again - that's MY excuse, anyway) but we're not dead
> yet...
>
I second that. And it would be great to have a genbank export module
(I remember even starting on that at one point...).
Looking forward to Frederic's Locustlink and genbank export code!
best,
Nico
> Thanks!
>
> Sean
>
> P.S. I'm not sure about getting 24 extra hours in the day - I have a
> sneaking
> suspicion that the work day would just expand to compensate.
> That kilo of that pure laboratory-grade Caffeine in the chemical supply
> catalogs looks more appealing all the time...
>
> On Thursday 01 July 2004 01:30 am, Frederic.Fleche@aventis.com wrote:
>> Hello ,
>> I was busy during the last months so my Locuslink file is still under
>> construction, by the way, what is the way if I want to append my code
>> to
>> this directory :
>>
>>
>> http://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/
>> My question is : Does any one have a biophp module to automatically
>> convert
>> a fasta file into an embl or genbank file. Actually I use Bioperl to
>> do
>> that but I would be glad to do all in PHP. If it doesn't exist a
>> solution
>> yet I will try to take the time to build it. Ha It would be great if
>> the
>> days were 24 hours longer !!!!!!!
>>
>>
>> Thanks in advance
>> Fred
> _______________________________________________
> Biophp-dev mailing list
> Biophp-dev@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biophp-dev
>
From biophp-dev@bioinformatics.org Fri Jul 9 03:59:20 2004
From: biophp-dev@bioinformatics.org (yvan)
Date: Fri, 09 Jul 2004 12:59:20 +1000
Subject: [Biophp-dev] hmmpfam parser
Message-ID:
Hi All,
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
From biophp-dev@bioinformatics.org Fri Jul 9 17:42:56 2004
From: biophp-dev@bioinformatics.org (Nico Stuurman)
Date: Fri, 9 Jul 2004 09:42:56 -0700
Subject: [Biophp-dev] hmmpfam parser
In-Reply-To:
References:
Message-ID: <07E3B714-D1C7-11D8-A66F-000D93ACBC76@itsa.ucsf.edu>
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
>
From biophp-dev@bioinformatics.org Sun Jul 11 06:54:52 2004
From: biophp-dev@bioinformatics.org (Nico Stuurman)
Date: Sat, 10 Jul 2004 22:54:52 -0700
Subject: [Biophp-dev] Added function Tm
In-Reply-To: <200407011051.25971.mail-lists+biophpdev@dogphilosophy.net>
References: <53D963F97CB58646886BEAFC25E0FAFB02FC9B@crbsmxsusr02.pharma.aventis.com> <200407011051.25971.mail-lists+biophpdev@dogphilosophy.net>
Message-ID:
I added a function Tm that calculates the melting temp for a given DNA
duplex. It can use either a 'basic', a salt dependent ('sa') or
nearest-neighbor method to calculate the Tm. The function is in
functions/seq.inc.php, and there is also a link in the class nucseq.
Let me know if you have problems with it.
Best,
Nico
From biophp-dev@bioinformatics.org Sun Jul 11 23:29:42 2004
From: biophp-dev@bioinformatics.org (yvan)
Date: Mon, 12 Jul 2004 08:29:42 +1000
Subject: [Biophp-dev] hmmpfam parser
In-Reply-To: <07E3B714-D1C7-11D8-A66F-000D93ACBC76@itsa.ucsf.edu>
References:
<07E3B714-D1C7-11D8-A66F-000D93ACBC76@itsa.ucsf.edu>
Message-ID:
Hi Nico,
Thank you for the answer, I will have a look at PEAR.
Were you in Basel in the 90th, at the Biocenter, third or fourth floor?
Just wondering your name rings some bells?
Cheers
Yvan
On 10/07/2004, at 2:42 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
From biophp-dev@bioinformatics.org Wed Jul 14 17:42:02 2004
From: biophp-dev@bioinformatics.org (Nico Stuurman)
Date: Wed, 14 Jul 2004 09:42:02 -0700
Subject: [Biophp-dev] hmmpfam parser
In-Reply-To:
References: <07E3B714-D1C7-11D8-A66F-000D93ACBC76@itsa.ucsf.edu>
Message-ID:
Hi Yvan,
That is right. I was in Ueli Aebi's lab on the third floor between
roughly '94 and '98. Remind me where you were during that time...
(and it would be fun to hear what you are doing now in Australia - at
least that is what your email address suggests).
best,
Nico
On Jul 11, 2004, at 3:29 PM, yvan wrote:
> Hi Nico,
>
> Thank you for the answer, I will have a look at PEAR.
>
> Were you in Basel in the 90th, at the Biocenter, third or fourth
> floor? Just wondering your name rings some bells?
>
> Cheers
>
> Yvan
>
>
> On 10/07/2004, at 2:42 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
>
> _______________________________________________
> Biophp-dev mailing list
> Biophp-dev@bioinformatics.org
> https://bioinformatics.org/mailman/listinfo/biophp-dev
>
From biophp-dev@bioinformatics.org Thu Jul 15 00:23:53 2004
From: biophp-dev@bioinformatics.org (yvan)
Date: Thu, 15 Jul 2004 09:23:53 +1000
Subject: [Biophp-dev] hmmpfam parser
In-Reply-To:
References:
<07E3B714-D1C7-11D8-A66F-000D93ACBC76@itsa.ucsf.edu>
Message-ID:
Hello Nico,
I was in Walter Keller's lab on the second floor. And now working for
the victorian bioinformatics consortium in Melbourne, trying to
annotate some funny down under genomes, wallaby, platypus, or scabies.
The Aebi lab had a nice scanner i was using. And you how is
California??
Cheers,
yvan
On 15/07/2004, at 2:42 AM, Nico Stuurman wrote:
> Hi Yvan,
>
> That is right. I was in Ueli Aebi's lab on the third floor between
> roughly '94 and '98. Remind me where you were during that time...
> (and it would be fun to hear what you are doing now in Australia - at
> least that is what your email address suggests).
>
> best,
>
>
> Nico
From biophp-dev@bioinformatics.org Thu Jul 15 01:59:23 2004
From: biophp-dev@bioinformatics.org (dong gregorio)
Date: Thu, 15 Jul 2004 08:59:23 +0800
Subject: [Biophp-dev] hmmpfam parser
Message-ID: <20040715005923.C2EEE3384B@ws7-3.us4.outblaze.com>
Hi all!
Sorry for being so quiet lately. I've been rather busy at work. On the other hand, it's a good thing 'coz some rather interesting ideas have been "incubating" for the time being...
Btw, I met some of the BioPerl "gods" last week... 'twas an interesting encounter... of course, I did my best to plug BioPHP... =)
Serge
----- Original Message -----
From: Nico Stuurman
Date: Wed, 14 Jul 2004 09:42:02 -0700
To: biophp-dev@bioinformatics.org
Subject: Re: [Biophp-dev] hmmpfam parser
> Hi Yvan,
>
> That is right. I was in Ueli Aebi's lab on the third floor between
> roughly '94 and '98. Remind me where you were during that time...
> (and it would be fun to hear what you are doing now in Australia - at
> least that is what your email address suggests).
>
> best,
>
>
> Nico
>
>
> On Jul 11, 2004, at 3:29 PM, yvan wrote:
>
> > Hi Nico,
> >
> > Thank you for the answer, I will have a look at PEAR.
> >
> > Were you in Basel in the 90th, at the Biocenter, third or fourth
> > floor? Just wondering your name rings some bells?
> >
> > Cheers
> >
> > Yvan
> >
> >
> > On 10/07/2004, at 2:42 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
--
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From biophp-dev@bioinformatics.org Mon Jul 26 22:09:09 2004
From: biophp-dev@bioinformatics.org (S Clark)
Date: Mon, 26 Jul 2004 15:09:09 -0600
Subject: [Biophp-dev] hmmpfam parser
In-Reply-To: <07E3B714-D1C7-11D8-A66F-000D93ACBC76@itsa.ucsf.edu>
References: <07E3B714-D1C7-11D8-A66F-000D93ACBC76@itsa.ucsf.edu>
Message-ID: <200407261509.12474.mail-lists+biophpdev@dogphilosophy.net>
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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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