get.seq with db='swissprot'

[Lars Skjærven]

Could we reconsider limiting input IDs to 6 chars for db='swissprot' in get.seq?

> get.seq("TCPA_YEAST", db="swissprot")
trying URL 'http://www.uniprot.org/uniprot/TCPA_Y.fasta'
Error in download.file(get.files[k], outfile, mode = "a") : 
  cannot open URL 'http://www.uniprot.org/uniprot/TCPA_Y.fasta'
In addition: Warning messages:
1: In get.seq("TCPA_YEAST", db = "swissprot") :
  ids should be standard 6 character SWISSPROT/UNIPROT formart: trying first 6 char...
2: In get.seq("TCPA_YEAST", db = "swissprot") :

Seems like the full length uniprot ID can be used:

download.file("http://www.uniprot.org/uniprot/TCPA_YEAST.fasta", tempfile())
trying URL 'http://www.uniprot.org/uniprot/TCPA_YEAST.fasta'
Content type 'text/plain' length 700 bytes
opened URL
==================================================
downloaded 700 bytes

[Xinqiu Yao]

That's a good point. I think we should remove the limiting here, which is only meaningful when it represents a PDB ID.

[Barry Grant]

agreed...

[Xinqiu Yao]

It seems resolved by this commit. Let me know if it is not.

[Lars Skjærven]

its not

[Xinqiu Yao]

Sorry for the confusing. Please see the amendment in this commit

get.seq("TCPA_YEAST", db="swissprot")
                       1        .         .         .         .         50 
sp|P12612|TCPA_YEAST   MSQLFNNSRSDTLFLGGEKISGDDIRNQNVLATMAVANVVKSSLGPVGLD
                       1        .         .         .         .         50 

                      51        .         .         .         .         100 
sp|P12612|TCPA_YEAST   KMLVDDIGDFTVTNDGATILSLLDVQHPAGKILVELAQQQDREIGDGTTS
                      51        .         .         .         .         100 

                     101        .         .         .         .         150 
sp|P12612|TCPA_YEAST   VVIIASELLKRANELVKNKIHPTTIITGFRVALREAIRFINEVLSTSVDT
                     101        .         .         .         .         150 

                     151        .         .         .         .         200 
sp|P12612|TCPA_YEAST   LGKETLINIAKTSMSSKIIGADSDFFSNMVVDALLAVKTQNSKGEIKYPV
                     151        .         .         .         .         200 

                     201        .         .         .         .         250 
sp|P12612|TCPA_YEAST   KAVNVLKAHGKSATESLLVPGYALNCTVASQAMPKRIAGGNVKIACLDLN
                     201        .         .         .         .         250 

                     251        .         .         .         .         300 
sp|P12612|TCPA_YEAST   LQKARMAMGVQINIDDPEQLEQIRKREAGIVLERVKKIIDAGAQVVLTTK
                     251        .         .         .         .         300 

                     301        .         .         .         .         350 
sp|P12612|TCPA_YEAST   GIDDLCLKEFVEAKIMGVRRCKKEDLRRIARATGATLVSSMSNLEGEETF
                     301        .         .         .         .         350 

                     351        .         .         .         .         400 
sp|P12612|TCPA_YEAST   ESSYLGLCDEVVQAKFSDDECILIKGTSKHSSSSIILRGANDYSLDEMER
                     351        .         .         .         .         400 

                     401        .         .         .         .         450 
sp|P12612|TCPA_YEAST   SLHDSLSVVKRTLESGNVVPGGGCVEAALNIYLDNFATTVGSREQLAIAE
                     401        .         .         .         .         450 

                     451        .         .         .         .         500 
sp|P12612|TCPA_YEAST   FAAALLIIPKTLAVNAAKDSSELVAKLRSYHAASQMAKPEDVKRRSYRNY
                     451        .         .         .         .         500 

                     501        .         .         .         .         550 
sp|P12612|TCPA_YEAST   GLDLIRGKIVDEIHAGVLEPTISKVKSLKSALEACVAILRIDTMITVDPE
                     501        .         .         .         .         550 

                     551       559 
sp|P12612|TCPA_YEAST   PPKEDPHDH
                     551       559 

Call:
  read.fasta(file = outfile)

Class:
  fasta

Alignment dimensions:
  1 sequence rows; 559 position columns (559 non-gap, 0 gap) 

+ attr: id, ali, call

[Xinqiu Yao]

Is this issue solved by the commit mentioned above?

[Lars Skjærven]

should be :) thanks !