[ensembl-dev] Converting cDNA position to genomic position!
Oyediran Akinrinade
oyediran.akinrinade at helsinki.fi
Fri Nov 23 13:25:18 GMT 2012
Hello,
Thanks for the help, it's now working perfectly! However, it seems to
be reporting the coordinates for genes transcribed in the reverse
direction in a way different from what is available on ensembl.org web
interface.
For instance,
curl 'http://beta.rest.ensembl.org/map/cdna/ENST00000218516/1..2?'" -H
'Content-type:application/json'
yields:
"('ENST00000218516', 1)","{u'mappings': [{u'end': 100662913, u'start':
100662912, u'coord_system': u'chromosome', u'rank': 0, u'gap': 0,
u'seq_region_name': u'X', u'strand': -1}]}"
cDNAcodingStart cDNAcodingEnd GenomiccodingStart Genomic coding end
23 216 100662698 100662891
The "end" in the output however corresponds to the Exon Chr End (bp)
from the ensembl.org webpage. Thus reporting the genomic cordinate of
cDNA pos 216 (i.e end of 1st coding cDNA) as the Exon Chr Start (bp.
It however works well for transcripts on the + strand and are
transcribed in the forward direction.
This makes the results unreliable in a way. Is there a way to make it
get all the genomic position/coordinates in a uniform direction
irrespective of the strand and direction of transcription?
Thanks for your anticipated support.
_Diran
Quoting "Andy Yates" <ayates at ebi.ac.uk>:
> Hi,
>
> We limit the rest service to a maximum of 3 requests per second over
> a hour and allow you to burst that limit by 6. If you sleep every 3
> requests for the remainder of the second you are on your issue will
> go e.g.
>
> import time
>
> then = time.time()
> time.sleep(0.1)
> now = time.time()
> diff = now - then
> if diff <= 1.0:
> sleep_time = 1.0 - diff
> time.sleep(sleep_time)
> print 'I went to sleep for '+str(sleep_time)+' seconds'
> print diff
>
>
> This way you only sleep for as long as you need to. You'll also have
> to combine this with a request counter to ensure you only sleep
> every 3 requests.
>
> HTH
>
> Andy
>
> Andrew Yates Ensembl Core Software Project Leader
> EMBL-EBI Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK http://www.ensembl.org/
>
> On 22 Nov 2012, at 14:07, Oyediran Akinrinade wrote:
>
>> Hello,
>>
>> Thanks for the help/info!
>>
>> I tried using the REST API but it keeps stopping without
>> completing. Here is my script for the query:
>>
>> #!/usr/bin/python
>>
>> import httplib2, sys
>> http = httplib2.Http(".cache")
>>
>> map=[]
>> f=open("EXTRACTED_FILE.txt","a") ## file open in appending mode i.e 'a'
>>
>> file=open('card_complete.txt', 'rU')
>> lines=file.readlines()
>> for line in lines:
>> transcript, start = line.split('\t')
>> start=int(start)
>> end=start+1
>> m=(transcript,start)
>> map.append(m)
>> server = "http://beta.rest.ensembl.org"
>> #ext = "/map/cdna/ENST00000379802/5513..5514?"
>> #ext = "/map/cdna/transcript/start..end?"
>> ext="/map/cdna/"+transcript+"/"+str(start)+".."+str(end)+"?"
>> resp, content = http.request(server+ext, method="GET",
>> headers={"Content-Type":"application/json"})
>> if not resp.status == 200:
>> print "Invalid response: ", resp.status
>> sys.exit()
>> import json
>> decoded = json.loads(content)
>> print "fetching", m, "now"
>> #f=open("EXTRACTED_FILE.txt","a") ## file open in appending mode i.e 'a'
>> f.write(repr(decoded)) ## writing the contain decoded to file
>> #print repr(decoded)
>> #print decoded
>> f.close()
>> print "completed"
>>
>> And it only works for few:
>>
>> fetching ('ENST00000070846', 76) now
>> fetching ('ENST00000070846', 84) now
>> fetching ('ENST00000070846', 156) now
>> fetching ('ENST00000070846', 176) now
>> fetching ('ENST00000070846', 184) now
>> fetching ('ENST00000070846', 193) now
>> fetching ('ENST00000070846', 227) now
>> fetching ('ENST00000070846', 235) now
>> fetching ('ENST00000070846', 258) now
>> fetching ('ENST00000070846', 259) now
>> fetching ('ENST00000070846', 275) now
>> fetching ('ENST00000070846', 302) now
>> Invalid response: 429
>>
>> # if not resp.status == 200:
>> print "Invalid response: ", resp.status
>> sys.exit()
>>
>> Do you have an idea of what could be wrong here?
>>
>>
>>
>> Quoting "Andy Yates" <ayates at ebi.ac.uk>:
>>
>>> Hi,
>>>
>>> You can also use the REST API which can map from protein, cds and
>>> cDNA to genomic locations:
>>>
>>> http://beta.rest.ensembl.org/map/cdna/ENST00000373968/123..554?content-type=application/json
>>>
>>> Brings back
>>>
>>> {"mappings":[{"seq_region_name":"10","gap":0,"coord_system":"chromosome","strand":-1,"rank":0,"end":54531338,"start":54531209},{"seq_region_name":"10","gap":0,"coord_system":"chromosome","strand":-1,"rank":0,"end":54530546,"start":54530430},{"seq_region_name":"10","gap":0,"coord_system":"chromosome","strand":-1,"rank":0,"end":54529075,"start":54529007},{"seq_region_name":"10","gap":0,"coord_system":"chromosome","strand":-1,"rank":0,"end":54528270,"start":54528155}]}
>>>
>>> The REST API is rate limited to 3 mappings per second so using the
>>> Perl API will give you a higher throughput
>>>
>>> Andy
>>>
>>> Andrew Yates Ensembl Core Software Project Leader
>>> EMBL-EBI Tel: +44-(0)1223-492538
>>> Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
>>> Cambridge CB10 1SD, UK http://www.ensembl.org/
>>>
>>> On 15 Nov 2012, at 10:59, Will McLaren wrote:
>>>
>>>> Hello Oyediran,
>>>>
>>>> You will need to use a TranscriptMapper object;
>>>> http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1TranscriptMapper.html
>>>>
>>>> The method you should use is cdna2genomic. Note that this returns
>>>> an array of coordinate objects; this is useful to know if, for
>>>> example, your coordinates only partially overlap the transcript.
>>>>
>>>> Here's a bit of code to get you started:
>>>>
>>>> my $reg = 'Bio::EnsEMBL::Registry';
>>>> $reg->load_registry_from_db(-host =>
>>>> 'ensembldb.ensembl.org',-user => 'anonymous');
>>>>
>>>> my $ta = $reg->get_adaptor('human','core','transcript');
>>>>
>>>> my $t = $ta->fetch_by_stable_id('ENST00000373968');
>>>>
>>>> my $mapper = Bio::EnsEMBL::TranscriptMapper->new($t);
>>>>
>>>> @coords = $trmapper->cdna2genomic( 123, 554 );
>>>>
>>>> Regards
>>>>
>>>> Will McLaren
>>>> Ensembl Variation
>>>>
>>>>
>>>> On 15 November 2012 10:45, Oyediran Akinrinade
>>>> <oyediran.akinrinade at helsinki.fi> wrote:
>>>>
>>>>
>>>> Hello,
>>>>
>>>> I have a list of ensembl transcripts IDs with their corresponding cDNA
>>>> positions and I will like to get their genomic positions using the
>>>> ensembl API. I have no experience with perl although I have
>>>> installed ensembl-api on my mac computer. There are about 6000 IDs
>>>> that I will like to get their genomic cordinates/positions, and
>>>> web-based queries will not be the best solution. To this end, I
>>>> write to request for your assistance.
>>>>
>>>> Looking forward to hearing from you soonest.
>>>>
>>>> Thanks,
>>>>
>>>> -Oyediran
>>>>
>>>>
>>>>
>>>>
>>>>
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>>>
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>>
>>
>>
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>
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