如何制作帶有FASTA格式參數的R函數

Question

這是我寫的代碼。 我試圖用FASTA格式的參數運行此函數，但此方法不起作用。 請幫助我更改代碼中的某些內容，以便可以輕松使用FASTA格式的參數進行計算

I= 131.1736 
L= 131.1736 
K= 146.1882 
M= 149.2124 
F= 165.19
T= 119.1197 
W= 204.2262 
V= 117.1469 
R= 174.2017 
H= 155.1552 
A= 89.0935
N= 132.1184 
D= 133.1032 
C= 121.159 
E= 147.1299 
Q= 146.1451 
G= 75.0669
P= 115.131
S= 105.093
Y= 181.1894


ref=c(I= 131.1736, L= 131.1736, K= 146.1882, M= 149.2124, F= 165.19, T= 119.1197, W= 204.2262, V= 117.1469, R= 174.2017, H= 155.1552, A= 89.0935, N= 132.1184, D= 133.1032, C= 121.159, E= 147.1299, Q= 146.1451, G= 75.0669, P= 115.131, S= 105.093, Y= 181.1894)

#function to calculate molecular weights of amino acids, could be used by using ("",ref=ref)

mw=function(compound)
{
    molecules=unlist(strsplit(compound,""))
    ans=sum(ref[molecules])-((nchar(compound)-1)*18)
    return(c("Molecular Weight:"=ans))
}

Answer 1

使用鏈接的fasta中的數據時，需要刪除新行"\\n" 。 添加了一個過濾器以刪除ref中沒有的任何字符。

# reference lookup
ref <- c(I = 131.1736, L = 131.1736, K = 146.1882, M = 149.2124, F = 165.19,
         T = 119.1197, W = 204.2262, V = 117.1469, R = 174.2017, H = 155.1552,
         A = 89.0935, N = 132.1184, D = 133.1032, C = 121.159, E = 147.1299,
         Q = 146.1451, G = 75.0669, P = 115.131, S = 105.093, Y = 181.1894)

mw <- function(compound){
  molecules <- unlist(strsplit(compound, ""))

  # keep only letters that appear in ref
  molecules <- molecules[ molecules %in% names(ref) ]

  ans <- sum(ref[molecules]) - ((nchar(compound)-1) * 18)
  #return
  paste("Molecular Weight: =", ans)
}

mw("ILK")
# [1] "Molecular Weight: = 372.5354"

mw("MNSMADTDRVNLTPIQRASEKSVQYHLKQVIGRGSYGVVYKAINKHTDQVVAIKEVVYENDEELNDIMAEISLLKNLNHNNIVKYHGFIRKSYELYILLE")
# [1] "Molecular Weight: = 11583.6644"

mw(c("ILL", "LKKS"))
# [1] "Molecular Weight: = 886.1638" "Molecular Weight: = 868.1638"

# this one has "new line \n" which will be dropped
mw("MN\nISLL")
# [1] "Molecular Weight: = 671.9446"