Bug with blast.pdb() / get.blast()
Issue #573
resolved
Evalues are incorrect.
> library(bio3d)
> p<-read.pdb("5p21")
>b<-blast.pdb(pdbseq(p))
Warning message:
In scan(file = file, what = what, sep = sep, quote = quote, dec = dec, :
EOF within quoted string
> head( b$raw$evalue )
[1] 344 344 343 343 343 343
> download.file(b$url, destfile="checkme.csv")
> tbl <- read.csv("checkme.csv", header=F)
> tbl[1:6,c(2,11)]
V2 V11
1 6AXG_B 2.94e-123
2 6Q21_A 3.43e-123
3 6AMB_A 4.26e-123
4 1WQ1_R 4.27e-123
5 5E95_A 4.95e-123
6 4NYI_R 5.63e-123
From looking at code it looks like the error is an extra quote character " in the get.blast() function. i.e the line
raw <- try(read.csv(urlget, header = FALSE, sep = ",",
quote = "\\"", dec = ".", fill = TRUE, comment.char = "",
stringsAsFactors = FALSE), silent = TRUE)
Should have quote = "\\",
and not quote = "\\"",
I am not sure how to fix can get back to codebase.
Comments (2)
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should be fixed with commit ed6feed
please try with the development version of bio3d