Hi Leo,
This bug is now fixed .
JGI2 was being incorrectly returned previously.
The correct style is JGI2.F and from now on, it will always check only
for JGI2.F
> library(GenomeInfoDb)
> seqlevelsStyle("T")
[1] "JGI2.F"
> seqlevelsStyle("LGI")
[1] "NCBI"
> mapSeqlevels('LGI', 'JGI2.F')
[1] "T"
> packageVersion("GenomeInfoDb")
[1] ‘1.3.4’
Thanks for pointing these out.
Best,
Sonali.
On 10/23/2014 3:35 PM, Leonardo Collado Torres wrote:
Hi,
I just found a tiny bug in .guessSpeciesStyle(). Basically, if the
style name has a dot, this function incorrectly returns the name of
the style.
See below:
## Lets guess the species and style for 'T'
GenomeInfoDb:::.guessSpeciesStyle('T')
$species
[1] "Populus trichocarpa"
$style
[1] "JGI2"
## Same style with the higher lvl function
seqlevelsStyle('T')
[1] "JGI2"
## Ok, style 'JGI2'
## In more dtail, this matches 'LGI' in NCBI style for this organism
GenomeInfoDb:::.supportedSeqnameMappings()["Populus_trichocarpa"]
$Populus_trichocarpa
NCBI JGI2.F
1 LGI T
2 LGII 2
3 LGIII 3
4 LGIV 4
5 LGV 5
6 LGVI 6
7 LGVII 7
8 LGVIII 8
9 LGIX 9
10 LGX 10
11 LGXI 11
12 LGXII 12
13 LGXIII 13
14 LGIV 14
15 LGXV 15
16 LGVI 16
17 LGVII 17
18 LGVIII 18
19 LGXIX 19
20 Pltd <NA>
## Guessing 'LGI' with the higher lvl function works
seqlevelsStyle('LGI')
[1] "NCBI"
## Mapping from 'LGI' in 'NCBI' style to 'JGI2' style doesn't work
mapSeqlevels('LGI', 'JGI2')
Error in mapSeqlevels("LGI", "JGI2") :
supplied seqname style "JGI2" is not supported
## Using the correct 'style' name works.
## However a user might have expected it to work with 'JGI2' given
## that this was the output from seqlevelsStyle('T')
mapSeqlevels('LGI', 'JGI2.F')
[1] "T"
## Although a user could find the correct name
head(genomeStyles('Populus trichocarpa'), 1)
circular auto sex NCBI JGI2.F
1 FALSE TRUE FALSE LGI T
packageVersion('GenomeInfoDb')
[1] ‘1.3.3’
Cheers,
Leo
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