fetch random id
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yvan
Nov 13, 2009, 10:02:00 AM11/13/09
to Group-4-Bioinformatics
Hello List,
I have to crash test a webservice so was wondering if any one knows a
way to get random sequence id from swissprot or genbank?
Thank for your help.
yvan
I have to crash test a webservice so was wondering if any one knows a
way to get random sequence id from swissprot or genbank?
Thank for your help.
yvan
zeeann g
Nov 13, 2009, 4:14:38 PM11/13/09
to group4bioi...@googlegroups.com
Its hard to understand ur issue Mr. Yvan. Kindly elaborate it.
-GRV
--
Related website : www.bioinformatics.fr
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yvan
Nov 20, 2009, 3:42:18 AM11/20/09
to group4bioi...@googlegroups.com
zeeann g wrote:
> Its hard to understand ur issue Mr. Yvan. Kindly elaborate it.
>
> -GRV
>
> On Fri, Nov 13, 2009 at 8:32 PM, yvan <yvan....@gmail.com
> <mailto:yvan....@gmail.com>> wrote:
>
> Hello List,
>
> I have to crash test a webservice so was wondering if any one knows a
> way to get random sequence id from swissprot or genbank?
> Thank for your help.
>
> yvan
>
> --
> Related website : www.bioinformatics.fr
> <http://www.bioinformatics.fr/>
> Its hard to understand ur issue Mr. Yvan. Kindly elaborate it.
>
> -GRV
>
> On Fri, Nov 13, 2009 at 8:32 PM, yvan <yvan....@gmail.com
> <mailto:yvan....@gmail.com>> wrote:
>
> Hello List,
>
> I have to crash test a webservice so was wondering if any one knows a
> way to get random sequence id from swissprot or genbank?
> Thank for your help.
>
> yvan
>
> --
> Related website : www.bioinformatics.fr
>
> You received this message because you are subscribed to the Google
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>
>
> --
> Related website : www.bioinformatics.fr
>
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Hello,
> http://groups.google.com/group/group4bioinformatics
>
>
> --
> Related website : www.bioinformatics.fr
>
> You received this message because you are subscribed to the Google
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I am writing some tests to find weak points or exceptions for a
webservice and/or a web application. The application takes a sequence in
fasta format and apply some "magic" on it. In order to find situations
which could crash the services, I am sending hundreds sequences
completely randomly chosen to the application.
Brad and Peter from the biopython community gave me good pointers,
especially Brad who suggested to use the random entry retrieval URL from
expasy.
http://www.expasy.org/cgi-bin/get-random-entry.pl?S
So now the problem is solved ;-)
But thanks anyway for asking.
Cheers
yvan
Fred
Nov 20, 2009, 8:49:02 AM11/20/09
to Group-4-Bioinformatics
Hello Yvan,
I know my response is too late 5Sorry I was in vacation) but anyway
here is what would be my suggestion using php.
1) Downloading all the Uniprot ID. (Should be available at :
http://www.uniprot.org/downloads).
2) Put all the Uniprot ID on a php array called $arrUniprotId.
3) Use the php function array_rand (http://php.net/manual/en/
function.array-rand.php) to get randomly an id : $myRandomId =
array_rand ($arrUniprotId);
4) Then create a set od url using a loop.
for($i = 0; $i <= 100; $i++) {
$myRandomUrl = "http://www.uniprot.org/uniprot/" . $myRandomId ;
}
Hope this helps,
Fred
On Nov 20, 9:42 am, yvan <yvan.str...@gmail.com> wrote:
> zeeann g wrote:
> > Its hard to understand ur issue Mr. Yvan. Kindly elaborate it.
>
> > -GRV
>
> yvan- Hide quoted text -
>
> - Show quoted text -
I know my response is too late 5Sorry I was in vacation) but anyway
here is what would be my suggestion using php.
1) Downloading all the Uniprot ID. (Should be available at :
http://www.uniprot.org/downloads).
2) Put all the Uniprot ID on a php array called $arrUniprotId.
3) Use the php function array_rand (http://php.net/manual/en/
function.array-rand.php) to get randomly an id : $myRandomId =
array_rand ($arrUniprotId);
4) Then create a set od url using a loop.
for($i = 0; $i <= 100; $i++) {
$myRandomUrl = "http://www.uniprot.org/uniprot/" . $myRandomId ;
}
Hope this helps,
Fred
On Nov 20, 9:42 am, yvan <yvan.str...@gmail.com> wrote:
> zeeann g wrote:
> > Its hard to understand ur issue Mr. Yvan. Kindly elaborate it.
>
> > -GRV
>
>
> - Show quoted text -
Luis-Miguel Rodríguez Rojas
Nov 21, 2009, 11:03:46 PM11/21/09
to group4bioi...@googlegroups.com
Hi Yvan,
The GIs from GenBank are assigned consecutively [1], and therefore you can use any random numbers generator to pick a number between 2 (there is no gi:1) and the latest GI (currently 269784792). To update the latest GI, you can use the Sequence Revision History [2], and try increasing your GI (the "first seen at NCBI" date is particularly useful for this end).
[1] http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html
[2] http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi
Hope it's useful,
Regards,--
Luis M. Rodriguez-R
[http://bioinf.uniandes.edu.co/~miguel/]
---------------------------------
Unidad de Bioinformática del Laboratorio de Micología y Fitopatología
Universidad de Los Andes, Colombia
[http://bioinf.uniandes.edu.co]
+ 57 1 3394949 ext 2619
luis...@uniandes.edu.co
lmrodr...@gmail.com
The GIs from GenBank are assigned consecutively [1], and therefore you can use any random numbers generator to pick a number between 2 (there is no gi:1) and the latest GI (currently 269784792). To update the latest GI, you can use the Sequence Revision History [2], and try increasing your GI (the "first seen at NCBI" date is particularly useful for this end).
[1] http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html
[2] http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi
Hope it's useful,
Regards,
Luis M. Rodriguez-R
[http://bioinf.uniandes.edu.co/~miguel/]
---------------------------------
Unidad de Bioinformática del Laboratorio de Micología y Fitopatología
Universidad de Los Andes, Colombia
[http://bioinf.uniandes.edu.co]
+ 57 1 3394949 ext 2619
luis...@uniandes.edu.co
lmrodr...@gmail.com
yvan
Nov 23, 2009, 6:22:55 AM11/23/09
to group4bioi...@googlegroups.com
Luis-Miguel Rodr�guez Rojas wrote:
> Hi Yvan,
>
> The GIs from GenBank are assigned consecutively [1], and therefore you
> can use any random numbers generator to pick a number between 2 (there
> is no gi:1) and the latest GI (currently 269784792). To update the
> latest GI, you can use the Sequence Revision History [2], and try
> increasing your GI (the "first seen at NCBI" date is particularly
> useful for this end).
>
> [1] http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html
> [2] http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi
>
> Hope it's useful,
>
> Regards,
>
> On Fri, Nov 20, 2009 at 8:49 AM, Fred <frederi...@gmail.com
> <mailto:frederi...@gmail.com>> wrote:
>
> Hello Yvan,
>
> I know my response is too late 5Sorry I was in vacation) but anyway
> here is what would be my suggestion using php.
> 1) Downloading all the Uniprot ID. (Should be available at :
> http://www.uniprot.org/downloads).
> 2) Put all the Uniprot ID on a php array called $arrUniprotId.
> 3) Use the php function array_rand (http://php.net/manual/en/
> function.array-rand.php
> <http://php.net/manual/en/%0Afunction.array-rand.php>) to get
> Hi Yvan,
>
> The GIs from GenBank are assigned consecutively [1], and therefore you
> can use any random numbers generator to pick a number between 2 (there
> is no gi:1) and the latest GI (currently 269784792). To update the
> latest GI, you can use the Sequence Revision History [2], and try
> increasing your GI (the "first seen at NCBI" date is particularly
> useful for this end).
>
> [1] http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html
> [2] http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi
>
> Hope it's useful,
>
> Regards,
>
> On Fri, Nov 20, 2009 at 8:49 AM, Fred <frederi...@gmail.com
> <mailto:frederi...@gmail.com>> wrote:
>
> Hello Yvan,
>
> I know my response is too late 5Sorry I was in vacation) but anyway
> here is what would be my suggestion using php.
> 1) Downloading all the Uniprot ID. (Should be available at :
> http://www.uniprot.org/downloads).
> 2) Put all the Uniprot ID on a php array called $arrUniprotId.
> 3) Use the php function array_rand (http://php.net/manual/en/
> function.array-rand.php
> randomly an id : $myRandomId =
> array_rand ($arrUniprotId);
> 4) Then create a set od url using a loop.
> for($i = 0; $i <= 100; $i++) {
> $myRandomUrl = "http://www.uniprot.org/uniprot/" . $myRandomId ;
> }
>
> Hope this helps,
>
> Fred
>
> On Nov 20, 9:42 am, yvan <yvan.str...@gmail.com
> array_rand ($arrUniprotId);
> 4) Then create a set od url using a loop.
> for($i = 0; $i <= 100; $i++) {
> $myRandomUrl = "http://www.uniprot.org/uniprot/" . $myRandomId ;
> }
>
> Hope this helps,
>
> Fred
>
> On Nov 20, 9:42 am, yvan <yvan.str...@gmail.com
> <mailto:yvan.str...@gmail.com>> wrote:
> > zeeann g wrote:
> > > Its hard to understand ur issue Mr. Yvan. Kindly elaborate it.
> >
> > > -GRV
> >
> > > On Fri, Nov 13, 2009 at 8:32 PM, yvan <yvan.str...@gmail.com
> <mailto:yvan.str...@gmail.com>
> > > <mailto:yvan.str...@gmail.com <mailto:yvan.str...@gmail.com>>>
> > zeeann g wrote:
> > > Its hard to understand ur issue Mr. Yvan. Kindly elaborate it.
> >
> > > -GRV
> >
> > > On Fri, Nov 13, 2009 at 8:32 PM, yvan <yvan.str...@gmail.com
> <mailto:yvan.str...@gmail.com>
> wrote:
> >
> > > Hello List,
> >
> > > I have to crash test a webservice so was wondering if any
> one knows a
> > > way to get random sequence id from swissprot or genbank?
> > > Thank for your help.
> >
> > > yvan
> >
> > > --
> > > Related website : www.bioinformatics.fr
> <http://www.bioinformatics.fr>
> > > <http://www.bioinformatics.fr/>
> >
> > > You received this message because you are subscribed to
> the Google
> > > Groups "group4bioinformatics" group.
> > > To post to this group, send email to
> > > group4bioi...@googlegroups.com
> <mailto:group4bioi...@googlegroups.com>
> > > <mailto:group4bioi...@googlegroups.com
> >
> > > Hello List,
> >
> > > I have to crash test a webservice so was wondering if any
> one knows a
> > > way to get random sequence id from swissprot or genbank?
> > > Thank for your help.
> >
> > > yvan
> >
> > > --
> > > Related website : www.bioinformatics.fr
> <http://www.bioinformatics.fr>
> > > <http://www.bioinformatics.fr/>
> >
> > > You received this message because you are subscribed to
> the Google
> > > Groups "group4bioinformatics" group.
> > > To post to this group, send email to
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> <mailto:group4bioi...@googlegroups.com>
> <mailto:group4bioi...@googlegroups.com>>
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> > > group4bioinforma...@googlegroups.com
> <mailto:group4bioinforma...@googlegroups.com>
> > > <mailto:group4bioinforma...@googlegroups.com
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> > > group4bioinforma...@googlegroups.com
> <mailto:group4bioinforma...@googlegroups.com>
> <mailto:group4bioinforma...@googlegroups.com>>
> > > For more options, visit this group at
> > > http://groups.google.com/group/group4bioinformatics
> >
> > > --
> > > Related website :www.bioinformatics.fr
> <http://www.bioinformatics.fr>
> > > For more options, visit this group at
> > > http://groups.google.com/group/group4bioinformatics
> >
> > > --
> > > Related website :www.bioinformatics.fr
> >
> > > You received this message because you are subscribed to the Google
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> <mailto:group4bioi...@googlegroups.com>
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> > > For more options, visit this group at
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> >
> > > You received this message because you are subscribed to the Google
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> >
> > Hello,
> >
> > I am writing some tests to find weak points or exceptions for a
> > webservice and/or a web application. The application takes a
> sequence in
> > fasta format and apply some "magic" on it. In order to find
> situations
> > which could crash the services, I am sending hundreds sequences
> > completely randomly chosen to the application.
> > Brad and Peter from the biopython community gave me good pointers,
> > especially Brad who suggested to use the random entry retrieval
> URL from
> > expasy.
> >
> > http://www.expasy.org/cgi-bin/get-random-entry.pl?S
> >
> > So now the problem is solved ;-)
> >
> > But thanks anyway for asking.
> > Cheers
> > yvan- Hide quoted text -
> >
> > - Show quoted text -
>
> --
> Related website : www.bioinformatics.fr
> <http://www.bioinformatics.fr>
> >
> > I am writing some tests to find weak points or exceptions for a
> > webservice and/or a web application. The application takes a
> sequence in
> > fasta format and apply some "magic" on it. In order to find
> situations
> > which could crash the services, I am sending hundreds sequences
> > completely randomly chosen to the application.
> > Brad and Peter from the biopython community gave me good pointers,
> > especially Brad who suggested to use the random entry retrieval
> URL from
> > expasy.
> >
> > http://www.expasy.org/cgi-bin/get-random-entry.pl?S
> >
> > So now the problem is solved ;-)
> >
> > But thanks anyway for asking.
> > Cheers
> > yvan- Hide quoted text -
> >
> > - Show quoted text -
>
> --
> Related website : www.bioinformatics.fr
>
> You received this message because you are subscribed to the Google
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>
>
>
>
> --
> <http://bioinf.uniandes.edu.co/%7Emiguel/>]
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>
>
>
>
> --
> ---------------------------------
> Unidad de Bioinform�tica del Laboratorio de Micolog�a y Fitopatolog�a
> luis...@uniandes.edu.co <mailto:luis...@uniandes.edu.co>
> lmrodr...@gmail.com <mailto:lmrodr...@gmail.com>
> --
> Related website : www.bioinformatics.fr
>
> You received this message because you are subscribed to the Google
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Hello,
What I am doing is:
> Related website : www.bioinformatics.fr
>
> You received this message because you are subscribed to the Google
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Hello,
1) fetch a random ID from expasy via this url
http://www.expasy.org/cgi-bin/get-random-entry.pl?S
2) fetch the records from this ID
3) manipulate the records in a way they are usable , for example switch
format, here swiss-prot to fasta
Maybe it is a little tedious, two fetches, but so I am sure I get a
existing, "real" protein. The code is completely dependant from expasy
and the consistency of the url's.
But it works ;-)
Thanks everyone for your help
Cheers,
yvan
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