Extracts data from a protein NMR experimental peak list. read_raw_file() function reads in a user provided protein NMR experimental peak list. It currently supports file format in csv, txt with deliminator of comma, whitespace or semicolon. Note: please don't leave space between sequence and chemical shifts data, otherwise it will report error.

Extracts data from a protein NMR experimental peak list. read_raw_file() function reads in a user provided protein NMR experimental peak list. It currently supports file format in csv, txt with deliminator of comma, whitespace or semicolon. Note: please don't leave space between sequence and chemical shifts data, otherwise it will report error.

read_raw_file(file_path, delim = "comma", assigned = FALSE)

Arguments

file_path	File path where input chemical shifts file is located
delim	Delimiter for parsing file
assigned	Flag tell whether the input chemical shifts file is already assigned or not

Value

A list contains protein sequence and chemical shift table.

Examples

input_type = "ws"
sample_data_generator(input_type = input_type)
head(read_raw_file("sample_input_ws.txt", delim="ws"))
#> Parsed with column specification:
#> cols(
#>   X1 = col_double(),
#>   X2 = col_double()
#> )
#> [[1]]
#> [1] "NHQDHNNFQTLPYVPCSTCEGNLACLSLCHIE"
#> 
#> [[2]]
#> # A tibble: 32 x 2
#>       X1    X2
#>    <dbl> <dbl>
#>  1  NA    38.6
#>  2  NA    28.8
#>  3  56.3  30.4
#>  4  54.4  41.3
#>  5  NA    28.8
#>  6  55.1  38.9
#>  7  NA    38.8
#>  8  NA    39.3
#>  9  NA    30.3
#> 10  62.1  69.8
#> # ... with 22 more rows
#> 
unlink("sample_input_ws.txt")

input_type = "csv"
sample_data_generator(input_type = input_type)
head(read_raw_file("sample_input.csv", delim="comma"))
#> Parsed with column specification:
#> cols(
#>   X1 = col_double(),
#>   X2 = col_double()
#> )
#> Warning: number of columns of result is not a multiple of vector length (arg 2)
#> Warning: 1 parsing failure.
#> row # A tibble: 1 x 5 col     row col   expected  actual    file               expected   <int> <chr> <chr>     <chr>     <chr>              actual 1    33 <NA>  2 columns 1 columns 'sample_input.csv' file # A tibble: 1 x 5
#> [[1]]
#> [1] "NHQDHNNFQTLPYVPCSTCEGNLACLSLCHIE"
#> 
#> [[2]]
#> # A tibble: 33 x 2
#>       X1    X2
#>    <dbl> <dbl>
#>  1  NA    38.6
#>  2  NA    28.8
#>  3  56.3  30.4
#>  4  54.4  41.3
#>  5  NA    28.8
#>  6  55.1  38.9
#>  7  NA    38.8
#>  8  NA    39.3
#>  9  NA    30.3
#> 10  62.1  69.8
#> # ... with 23 more rows
#> 
unlink("sample_input.csv")

input_type = "sc"
sample_data_generator(input_type = input_type)
head(read_raw_file("sample_input_sc.txt", delim="semicolon"))
#> Parsed with column specification:
#> cols(
#>   X1 = col_double(),
#>   X2 = col_double()
#> )
#> [[1]]
#> [1] "NHQDHNNFQTLPYVPCSTCEGNLACLSLCHIE"
#> 
#> [[2]]
#> # A tibble: 32 x 2
#>       X1    X2
#>    <dbl> <dbl>
#>  1  NA    38.6
#>  2  NA    28.8
#>  3  56.3  30.4
#>  4  54.4  41.3
#>  5  NA    28.8
#>  6  55.1  38.9
#>  7  NA    38.8
#>  8  NA    39.3
#>  9  NA    30.3
#> 10  62.1  69.8
#> # ... with 22 more rows
#> 
unlink("sample_input_sc.txt")