Bug with blast.pdb() / get.blast()

Issue #573 resolved
Former user created an issue

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.

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