Re: [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

2016-05-04 Thread Rainer Johannes 
Dear Martin, Lori,

I’ve added support for the column “tx_name” (which will return the transcript 
ID) to all ensembldb methods so that’s fine now. Apparently I was just a little 
late, since that is now in the devel version 1.5.1.

thanks, jo

> On 03 May 2016, at 18:51, Martin Morgan  wrote:
> 
> On 05/02/2016 03:46 AM, Rainer Johannes wrote:
>> Hi Herve,
>> 
>> passing down additional arguments to the internal exonsBy, cdsBy,
>> fiveUTRsByTranscript and threeUTRsByTranscript would do it! That
>> would be great, thanks.
> 
> Hi Johannes --
> 
> Lori (cc'd, a new team member) and I are working on this.
> 
> The easiest thing to do is add '...' to the transcriptLengths argument list, 
> and to pass this to transcripts, exonsBy, etc.
> 
> The only obstacle is that 'tx_name' (in the call to transcripts()) plays a 
> central role in TxDb, but is not supported by EnsDb. Is it reasonable for you 
> to add support for tx_name as a column (maybe a simple alias to tx_id, so no 
> need for schema change)?
> 
> Martin & Lori
> 
>> 
>> cheers, jo
>> 
>>> On 02 May 2016, at 07:38, Hervé Pagès 
>>> wrote:
>>> 
>>> Hi Johannes,
>>> 
>>> We can make transcriptLengths() a generic but isn't the situation
>>> similar to the extractTranscriptSeqs() situation that you brought
>>> in January
>>> (https://stat.ethz.ch/pipermail/bioc-devel/2016-January/008570.html)
>>> for which adding the ellipsis to the argument list of the function
>>> and proper forwarding of the extra arguments did the trick? In the
>>> case of transcriptLengths() the extra arguments would be forwarded
>>> to the internal calls to transcripts(), exonsBy(), cdsBy(),
>>> fiveUTRsByTranscript(), and threeUTRsByTranscript(), and so
>>> transcriptLengths() would work out-of-the-box on EnsDb objects.
>>> Would that work?
>>> 
>>> H.
>>> 
>>> On 04/30/2016 04:05 AM, Rainer Johannes wrote:
 Dear all,
 
 I was wondering, you think it would be possible to make the
 transcriptLength function in GenomicFeatures a method and export
 that? Reason is that I have also implemented a transcriptLength
 function (actually presently a method in order to allow that to
 be used for EnsDb and TxDb objects), but this causes the warning
 
 The following object is masked from 'package:GenomicFeatures':
 
 transcriptLengths
 
 on package loading.
 
 Just in case, that’s the code from my package:
 
 if(!isGeneric("transcriptLengths"))
 setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
 with.utr5_len=FALSE, with.utr3_len=FALSE, ...)
 standardGeneric("transcriptLengths”))
 setMethod("transcriptLengths", "EnsDb", function(x,
 with.cds_len=FALSE, with.utr5_len=FALSE, with.utr3_len=FALSE,
 filter=list()){ return(.transcriptLengths(x,
 with.cds_len=with.cds_len, with.utr5_len=with.utr3_len,
 with.utr3_len=with.utr3_len, filter=filter)) })
 
 
 cheers, jo
 
 
 ___
 Bioc-devel@r-project.org mailing list
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>>> 
>>> -- Hervé Pagès
>>> 
>>> Program in Computational Biology Division of Public Health
>>> Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave.
>>> N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024
>>> 
>>> E-mail: hpa...@fredhutch.org Phone:  (206) 667-5791 Fax:(206)
>>> 667-1319
>> 
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>> 
> 
> 
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Re: [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

2016-05-03 Thread Martin Morgan 

On 05/02/2016 03:46 AM, Rainer Johannes wrote:

Hi Herve,

passing down additional arguments to the internal exonsBy, cdsBy,
fiveUTRsByTranscript and threeUTRsByTranscript would do it! That
would be great, thanks.


Hi Johannes --

Lori (cc'd, a new team member) and I are working on this.

The easiest thing to do is add '...' to the transcriptLengths argument 
list, and to pass this to transcripts, exonsBy, etc.


The only obstacle is that 'tx_name' (in the call to transcripts()) plays 
a central role in TxDb, but is not supported by EnsDb. Is it reasonable 
for you to add support for tx_name as a column (maybe a simple alias to 
tx_id, so no need for schema change)?


Martin & Lori



cheers, jo


On 02 May 2016, at 07:38, Hervé Pagès 
wrote:

Hi Johannes,

We can make transcriptLengths() a generic but isn't the situation
similar to the extractTranscriptSeqs() situation that you brought
in January
(https://stat.ethz.ch/pipermail/bioc-devel/2016-January/008570.html)
for which adding the ellipsis to the argument list of the function
and proper forwarding of the extra arguments did the trick? In the
case of transcriptLengths() the extra arguments would be forwarded
to the internal calls to transcripts(), exonsBy(), cdsBy(),
fiveUTRsByTranscript(), and threeUTRsByTranscript(), and so
transcriptLengths() would work out-of-the-box on EnsDb objects.
Would that work?

H.

On 04/30/2016 04:05 AM, Rainer Johannes wrote:

Dear all,

I was wondering, you think it would be possible to make the
transcriptLength function in GenomicFeatures a method and export
that? Reason is that I have also implemented a transcriptLength
function (actually presently a method in order to allow that to
be used for EnsDb and TxDb objects), but this causes the warning

The following object is masked from 'package:GenomicFeatures':

transcriptLengths

on package loading.

Just in case, that’s the code from my package:

if(!isGeneric("transcriptLengths"))
setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
with.utr5_len=FALSE, with.utr3_len=FALSE, ...)
standardGeneric("transcriptLengths”))
setMethod("transcriptLengths", "EnsDb", function(x,
with.cds_len=FALSE, with.utr5_len=FALSE, with.utr3_len=FALSE,
filter=list()){ return(.transcriptLengths(x,
with.cds_len=with.cds_len, with.utr5_len=with.utr3_len,
with.utr3_len=with.utr3_len, filter=filter)) })


cheers, jo


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-- Hervé Pagès

Program in Computational Biology Division of Public Health
Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave.
N, M1-B514 P.O. Box 19024 Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org Phone:  (206) 667-5791 Fax:(206)
667-1319


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recipient(s), you are hereby notified that any disclosure, copying, 
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this message in error, please notify the sender immediately by e-mail and 
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Re: [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

2016-05-02 Thread Rainer Johannes 
Hi Herve,

passing down additional arguments to the internal exonsBy, cdsBy, 
fiveUTRsByTranscript and threeUTRsByTranscript would do it! That would be 
great, thanks.

cheers, jo

> On 02 May 2016, at 07:38, Hervé Pagès  wrote:
> 
> Hi Johannes,
> 
> We can make transcriptLengths() a generic but isn't the situation
> similar to the extractTranscriptSeqs() situation that you brought
> in January 
> (https://stat.ethz.ch/pipermail/bioc-devel/2016-January/008570.html) for 
> which adding the ellipsis to the argument list of the
> function and proper forwarding of the extra arguments did the trick?
> In the case of transcriptLengths() the extra arguments would be
> forwarded to the internal calls to transcripts(), exonsBy(), cdsBy(),
> fiveUTRsByTranscript(), and threeUTRsByTranscript(), and so
> transcriptLengths() would work out-of-the-box on EnsDb objects.
> Would that work?
> 
> H.
> 
> On 04/30/2016 04:05 AM, Rainer Johannes wrote:
>> Dear all,
>> 
>> I was wondering, you think it would be possible to make the transcriptLength 
>> function in GenomicFeatures a method and export that? Reason is that I have 
>> also implemented a transcriptLength function (actually presently a method in 
>> order to allow that to be used for EnsDb and TxDb objects), but this causes 
>> the warning
>> 
>> The following object is masked from 'package:GenomicFeatures':
>> 
>> transcriptLengths
>> 
>> on package loading.
>> 
>> Just in case, that’s the code from my package:
>> 
>> if(!isGeneric("transcriptLengths"))
>> setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
>>  with.utr5_len=FALSE,
>>  with.utr3_len=FALSE, ...)
>> standardGeneric("transcriptLengths”))
>> setMethod("transcriptLengths", "EnsDb", function(x, with.cds_len=FALSE, 
>> with.utr5_len=FALSE,
>> with.utr3_len=FALSE, 
>> filter=list()){
>> return(.transcriptLengths(x, with.cds_len=with.cds_len, 
>> with.utr5_len=with.utr3_len,
>>   with.utr3_len=with.utr3_len, filter=filter))
>> })
>> 
>> 
>> cheers, jo
>> 
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> 
> 
> -- 
> Hervé Pagès
> 
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
> 
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319

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Re: [Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

2016-05-01 Thread Hervé Pagès 

Hi Johannes,

We can make transcriptLengths() a generic but isn't the situation
similar to the extractTranscriptSeqs() situation that you brought
in January 
(https://stat.ethz.ch/pipermail/bioc-devel/2016-January/008570.html) for 
which adding the ellipsis to the argument list of the

function and proper forwarding of the extra arguments did the trick?
In the case of transcriptLengths() the extra arguments would be
forwarded to the internal calls to transcripts(), exonsBy(), cdsBy(),
fiveUTRsByTranscript(), and threeUTRsByTranscript(), and so
transcriptLengths() would work out-of-the-box on EnsDb objects.
Would that work?

H.

On 04/30/2016 04:05 AM, Rainer Johannes wrote:

Dear all,

I was wondering, you think it would be possible to make the transcriptLength 
function in GenomicFeatures a method and export that? Reason is that I have 
also implemented a transcriptLength function (actually presently a method in 
order to allow that to be used for EnsDb and TxDb objects), but this causes the 
warning

The following object is masked from 'package:GenomicFeatures':

 transcriptLengths

on package loading.

Just in case, that’s the code from my package:

if(!isGeneric("transcriptLengths"))
 setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
  with.utr5_len=FALSE,
  with.utr3_len=FALSE, ...)
 standardGeneric("transcriptLengths”))
setMethod("transcriptLengths", "EnsDb", function(x, with.cds_len=FALSE, 
with.utr5_len=FALSE,
 with.utr3_len=FALSE, 
filter=list()){
 return(.transcriptLengths(x, with.cds_len=with.cds_len, 
with.utr5_len=with.utr3_len,
   with.utr3_len=with.utr3_len, filter=filter))
})


cheers, jo


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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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[Bioc-devel] Making transcriptLength function a method in GenomicFeatures?

2016-04-30 Thread Rainer Johannes 
Dear all,

I was wondering, you think it would be possible to make the transcriptLength 
function in GenomicFeatures a method and export that? Reason is that I have 
also implemented a transcriptLength function (actually presently a method in 
order to allow that to be used for EnsDb and TxDb objects), but this causes the 
warning

The following object is masked from 'package:GenomicFeatures':

transcriptLengths

on package loading.

Just in case, that’s the code from my package:

if(!isGeneric("transcriptLengths"))
setGeneric("transcriptLengths", function(x, with.cds_len=FALSE,
 with.utr5_len=FALSE,
 with.utr3_len=FALSE, ...)
standardGeneric("transcriptLengths”))
setMethod("transcriptLengths", "EnsDb", function(x, with.cds_len=FALSE, 
with.utr5_len=FALSE,
with.utr3_len=FALSE, 
filter=list()){
return(.transcriptLengths(x, with.cds_len=with.cds_len, 
with.utr5_len=with.utr3_len,
  with.utr3_len=with.utr3_len, filter=filter))
})


cheers, jo


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