[ensembl-dev] Problem when retrieving CDS coordinates

[Joerg Fallmann]

Hi Andy,
thank you so very much, it seems to work now, would not have come up 
with this without your help!
Cheers,
Joerg

On 06/27/2012 03:52 PM, dev-request at ensembl.org wrote:
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> Today's Topics:
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>     1. Re: Dev Digest, Vol 24, Issue 45 (??)
>     2. Re: species names (Dan Staines)
>     3. Problem when retrieving CDS coordinates (Joerg Fallmann)
>     4. Re: Problem when retrieving CDS coordinates (Andy Yates)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 27 Jun 2012 20:14:25 +0800
> From: ??<danielchen06 at gmail.com>
> Subject: Re: [ensembl-dev] Dev Digest, Vol 24, Issue 45
> To: dev at ensembl.org
> Message-ID:
> 	<CABjKtWZARYUwoxRevSVoGVRDGfdMed_-HCtqSbLV_y7G7F7w=Q at mail.gmail.com>
> Content-Type: text/plain; charset="gb2312"
>
> Hi  Jonathan
>
> species name and abbreviation also can find
> in public-plugins/ensembl/conf/SiteDefs.pm
>
> Best
>
> Gang Chen
>
> 2012/6/27<dev-request at ensembl.org>
>
>> Send Dev mailing list submissions to
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>> or, via email, send a message with subject or body 'help' to
>>         dev-request at ensembl.org
>>
>> You can reach the person managing the list at
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>> When replying, please edit your Subject line so it is more specific
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>>
>>
>> Today's Topics:
>>
>>    1. species names (jonathan myles)
>>    2. Re: species names (Stephen Fitzgerald)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Wed, 27 Jun 2012 11:41:13 +0100
>> From: jonathan myles<jonathanmyles1 at googlemail.com>
>> Subject: [ensembl-dev] species names
>> To: dev at ensembl.org
>> Message-ID:
>>         <CAOXpw8LrWynbqB7du6gPH2h-9Gp41v2c0PfsQ2hLdTUirvZ9-g at mail.gmail.com
>> Content-Type: text/plain; charset=ISO-8859-1
>>
>> Hi
>>
>> Sorry, this is such an elementary one that I'm really  embarrassed
>> that I can't find it in the documentation
>>
>> For a given species, eg mycosphaerella graminicola, how do I find the
>> precise string which represents that species for querying the ENSEMBL
>> or compara databases?
>>
>> Thank you
>>
>> Jonathan
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Wed, 27 Jun 2012 11:57:41 +0100 (BST)
>> From: Stephen Fitzgerald<stephenf at ebi.ac.uk>
>> Subject: Re: [ensembl-dev] species names
>> To: Ensembl developers list<dev at ensembl.org>
>> Message-ID:<alpine.LRH.2.00.1206271150540.16190 at login-r6-1.ebi.ac.uk>
>> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>>
>> Hi Jonathan, running this on the command line should give you the species
>> names in compara-67, which you can then pipe in to grep for your species
>> of interest.
>>
>>
>> mysql -uanonymous -hensembldb.ensembl.org -P5306 -Densembl_compara_67
>> -e"select name from genome_db"
>> +-------------------------------+
>> | name                          |
>> +-------------------------------+
>> | ailuropoda_melanoleuca        |
>> | ancestral_sequences           |
>> | anolis_carolinensis           |
>> | bos_taurus                    |
>> | caenorhabditis_elegans        |
>> | callithrix_jacchus            |
>> | canis_familiaris              |
>> | cavia_porcellus               |
>> | choloepus_hoffmanni           |
>> | ciona_intestinalis            |
>> | ciona_savignyi                |
>> | danio_rerio                   |
>> | dasypus_novemcinctus          |
>> | dipodomys_ordii               |
>> | drosophila_melanogaster       |
>> | echinops_telfairi             |
>> | equus_caballus                |
>> | erinaceus_europaeus           |
>> | felis_catus                   |
>> | gadus_morhua                  |
>> | gallus_gallus                 |
>> | gasterosteus_aculeatus        |
>> | gorilla_gorilla               |
>> | homo_sapiens                  |
>> | latimeria_chalumnae           |
>> | loxodonta_africana            |
>> | macaca_mulatta                |
>> | macropus_eugenii              |
>> | meleagris_gallopavo           |
>> | microcebus_murinus            |
>> | monodelphis_domestica         |
>> | mus_musculus                  |
>> | myotis_lucifugus              |
>> | nomascus_leucogenys           |
>> | ochotona_princeps             |
>> | oreochromis_niloticus         |
>> | ornithorhynchus_anatinus      |
>> | oryctolagus_cuniculus         |
>> | oryzias_latipes               |
>> | otolemur_garnettii            |
>> | pan_troglodytes               |
>> | petromyzon_marinus            |
>> | pongo_abelii                  |
>> | procavia_capensis             |
>> | pteropus_vampyrus             |
>> | rattus_norvegicus             |
>> | saccharomyces_cerevisiae      |
>> | sarcophilus_harrisii          |
>> | sorex_araneus                 |
>> | spermophilus_tridecemlineatus |
>> | sus_scrofa                    |
>> | taeniopygia_guttata           |
>> | takifugu_rubripes             |
>> | tarsius_syrichta              |
>> | tetraodon_nigroviridis        |
>> | tupaia_belangeri              |
>> | tursiops_truncatus            |
>> | vicugna_pacos                 |
>> | xenopus_tropicalis            |
>> +-------------------------------+
>>
>>
>> On Wed, 27 Jun 2012, jonathan myles wrote:
>>
>>> Hi
>>>
>>> Sorry, this is such an elementary one that I'm really  embarrassed
>>> that I can't find it in the documentation
>>>
>>> For a given species, eg mycosphaerella graminicola, how do I find the
>>> precise string which represents that species for querying the ENSEMBL
>>> or compara databases?
>>>
>>> Thank you
>>>
>>> Jonathan
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> List admin (including subscribe/unsubscribe):
>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>
>>
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>> End of Dev Digest, Vol 24, Issue 45
>> ***********************************
>>
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