[biomart-users] Query size limit

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[biomart-users] Query size limit

Moretti Sebastien
Hi

I wonder if there is a limit in filter values, using web service.
Months ago I was able to send all chromosomal positions of a gene in a single query to check if some of them were SNPs.
It is not possible now for few months, I always get a timeout.

E.g.
<Filter name = "chromosomal_region" value = "1:89058116:89058116,1:89053454:89053454,1:89057129:89057129,1:89054805:89054805,1:89063134:89063134,1:89057072:89057072,1:89063201:89063201,1:89054737:89054737,1:89053440:89053440,1:89055166:89055166,1:89056953:89056953,1:89059008:89059008,1:89053429:89053429,1:89059423:89059423,1:89056915:89056915,
.........
1:89054792:89054792,1:89058866:89058866,1:89057090:89057090,1:89056947:89056947,1:89054729:89054729,1:89056162:89056162,1:89059319:89059319,1:89058083:89058083"/>

Regards
Sébastien Moretti

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Re: [biomart-users] Query size limit

Arek Kasprzyk
Hi Sebastien,

there is not query limit for filter values per se. However it is always a good practice to split your query in smaller chunks to be on the safe side. 

a.

On 30 June 2015 at 09:09, Moretti Sebastien <[hidden email]> wrote:
Hi

I wonder if there is a limit in filter values, using web service.
Months ago I was able to send all chromosomal positions of a gene in a single query to check if some of them were SNPs.
It is not possible now for few months, I always get a timeout.

E.g.
<Filter name = "chromosomal_region" value = "1:89058116:89058116,1:89053454:89053454,1:89057129:89057129,1:89054805:89054805,1:89063134:89063134,1:89057072:89057072,1:89063201:89063201,1:89054737:89054737,1:89053440:89053440,1:89055166:89055166,1:89056953:89056953,1:89059008:89059008,1:89053429:89053429,1:89059423:89059423,1:89056915:89056915,
.........
1:89054792:89054792,1:89058866:89058866,1:89057090:89057090,1:89056947:89056947,1:89054729:89054729,1:89056162:89056162,1:89059319:89059319,1:89058083:89058083"/>

Regards
Sébastien Moretti

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Re: [biomart-users] Query size limit

Moretti Sebastien
Hi Arek

Thanks, I will split my big query in several small ones.
Do you think 500 SNP positions per query is safe enough?

Regards
Sébastien


Hi Sebastien,

there is not query limit for filter values per se. However it is always a good practice to split your query in smaller chunks to be on the safe side. 

a.

On 30 June 2015 at 09:09, Moretti Sebastien <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="30Ini_MNX3oJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">moretti....@...> wrote:
Hi

I wonder if there is a limit in filter values, using web service.
Months ago I was able to send all chromosomal positions of a gene in a single query to check if some of them were SNPs.
It is not possible now for few months, I always get a timeout.

E.g.
<Filter name = "chromosomal_region" value = "1:89058116:89058116,1:89053454:89053454,1:89057129:89057129,1:89054805:89054805,1:89063134:89063134,1:89057072:89057072,1:89063201:89063201,1:89054737:89054737,1:89053440:89053440,1:89055166:89055166,1:89056953:89056953,1:89059008:89059008,1:89053429:89053429,1:89059423:89059423,1:89056915:89056915,
.........
1:89054792:89054792,1:89058866:89058866,1:89057090:89057090,1:89056947:89056947,1:89054729:89054729,1:89056162:89056162,1:89059319:89059319,1:89058083:89058083"/>

Regards
Sébastien Moretti

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Re: [biomart-users] Query size limit

Arek Kasprzyk

It should be. Yes

a

Sent from my iPhone

On 1 Jul 2015, at 10:37, Moretti Sebastien <[hidden email]> wrote:

Hi Arek

Thanks, I will split my big query in several small ones.
Do you think 500 SNP positions per query is safe enough?

Regards
Sébastien


Hi Sebastien,

there is not query limit for filter values per se. However it is always a good practice to split your query in smaller chunks to be on the safe side. 

a.

On 30 June 2015 at 09:09, Moretti Sebastien <<a href="javascript:" target="_blank" gdf-obfuscated-mailto="30Ini_MNX3oJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">moretti....@...> wrote:
Hi

I wonder if there is a limit in filter values, using web service.
Months ago I was able to send all chromosomal positions of a gene in a single query to check if some of them were SNPs.
It is not possible now for few months, I always get a timeout.

E.g.
<Filter name = "chromosomal_region" value = "1:89058116:89058116,1:89053454:89053454,1:89057129:89057129,1:89054805:89054805,1:89063134:89063134,1:89057072:89057072,1:89063201:89063201,1:89054737:89054737,1:89053440:89053440,1:89055166:89055166,1:89056953:89056953,1:89059008:89059008,1:89053429:89053429,1:89059423:89059423,1:89056915:89056915,
.........
1:89054792:89054792,1:89058866:89058866,1:89057090:89057090,1:89056947:89056947,1:89054729:89054729,1:89056162:89056162,1:89059319:89059319,1:89058083:89058083"/>

Regards
Sébastien Moretti

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That means you've stood up for something, sometime in your life.”

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