npjc / readyg

Read, Validate, Simulate and Write YeastGrower Files

Read, Validate, Simulate and Write YeastGrower (aka ACCESS) files.

Installation

# install.packages("readyg") # not yet.
remotes::install_github("npjc/readyg")

Example

Yeast Grower/ACCESS files are written in windows ini format (sort-of). read_yg() parses this format and returns the data in a format suitable for analysis or exporting (writing) to a .csv files.

library(readyg)
files <- yg_example_files()
read_yg(files[1])
#> # A tibble: 7,872 x 4
#>    plate well  runtime measure
#>    <dbl> <chr>   <dbl>   <dbl>
#>  1     1 A01       984   0.116
#>  2     1 A01      1868   0.121
#>  3     1 A01      2746   0.126
#>  4     1 A01      3622   0.122
#>  5     1 A01      4499   0.117
#>  6     1 A01      5375   0.122
#>  7     1 A01      6252   0.124
#>  8     1 A01      7128   0.119
#>  9     1 A01      8004   0.120
#> 10     1 A01      8881   0.118
#> # … with 7,862 more rows
read_yg(files[1], all_fields = TRUE) # full yg has quite a lot of fields...
#> # A tibble: 1 x 3
#>   data                 run_params         drug_data        
#>   <list>               <list>             <list>           
#> 1 <tibble [7,872 × 5]> <tibble [149 × 2]> <tibble [25 × 2]>

In the individual sections:

d <- read_yg(files[1], all_fields = TRUE)
d$data
#> [[1]]
#> # A tibble: 7,872 x 5
#>    well  datetime            runtime measure temperature
#>    <chr> <dttm>                <dbl>   <dbl>       <dbl>
#>  1 A01   2013-09-05 15:36:07     984   0.116        30.1
#>  2 A01   2013-09-05 15:50:52    1868   0.121        29.8
#>  3 A01   2013-09-05 16:05:30    2746   0.126        30  
#>  4 A01   2013-09-05 16:20:06    3622   0.122        29.8
#>  5 A01   2013-09-05 16:34:42    4499   0.117        30  
#>  6 A01   2013-09-05 16:49:19    5375   0.122        30  
#>  7 A01   2013-09-05 17:03:56    6252   0.124        30  
#>  8 A01   2013-09-05 17:18:32    7128   0.119        30  
#>  9 A01   2013-09-05 17:33:08    8004   0.120        30  
#> 10 A01   2013-09-05 17:47:44    8881   0.118        30  
#> # … with 7,862 more rows
d$run_params
#> [[1]]
#> # A tibble: 149 x 2
#>    key              value                
#>    <chr>            <chr>                
#>  1 file_origin      reconstructed_from_DB
#>  2 comments         no%20comment         
#>  3 plate_size       96                   
#>  4 screen_run_type  pre_screen_1         
#>  5 run_id           A                    
#>  6 save_data_file   RT1-79               
#>  7 run_plate_repeat 1                    
#>  8 parent_id        ""                   
#>  9 strain_name      ""                   
#> 10 media_name       ypd                  
#> # … with 139 more rows
d$drug_data
#> [[1]]
#> # A tibble: 25 x 2
#>    key              value    
#>    <chr>            <chr>    
#>  1 drug_plate       none     
#>  2 strain_plate     none     
#>  3 run_id           A        
#>  4 run_plate_repeat 1        
#>  5 parent_id        ""       
#>  6 user             elisa_ubc
#>  7 project_name     elisa_ubc
#>  8 media_name       ypd      
#>  9 quarter          A        
#> 10 time_frm_freezer -1       
#> # … with 15 more rows

If you want the information in the other sections , you can use read_ini() instead. This parses the ini file into a list:

l <- read_ini(files[1])
str(l, 1)
#> List of 6
#>  $ config file info:List of 1
#>  $ Run_Parameters  :List of 149
#>  $ Runtime_State   :List of 34
#>  $ Drug_Data       :List of 25
#>  $ Analysis        :List of 92
#>  $ Data:           :List of 83

Additional Info

YeastGrower/ACCESS encodes data in non-standard ways that read_yg() corrects:

data section:

• the temperature field may be written as 300, 30, 30.0 to indicate 30ºC.
• the datetime field in the data may be written as D0_12:11:10, D0 _12:11:10 or 12:11:10 to indicate 12:11:10 on the first day of the run. To indicate what date D0 is you can provide this as an argument to e.g. read_yg('path/to/file.txt', start_date = 'YYYY-MM-DD').
  • N.B. if the datetime field is encoded as 12:11:10 and the run last longer that one day the current results may be erroneous. e.g. 12:11:10, ... , 23:48:17, ... , 00:12:34 would be encoded as the same day. This is the safe default but will provide an option to ‘fix’ this in the future.
• well field: The well field is encoded in row-major order (‘standard’) for 6,24,96, and 384 well plates but ACCESS uses a custom ordering for 48 well plates. Currently, we remap these to the standard arangement so that the wells names of a 48-well plate follow the standard convention.
  • N.B. the drug_data section, if present, can contain a Well_Alias field which is currently not checked for this inconsistency. Handle with care if using this information.

all the keys

The Yeast Grower format has some use of nearly 3000 separte keys (fields). To retrieve all of them:

yg_section_keys()
#> # A tibble: 2,979 x 2
#>    section          key               
#>    <chr>            <chr>             
#>  1 config file info last_write        
#>  2 config file info last write        
#>  3 Run_Parameters   Instrument        
#>  4 Run_Parameters   Ini_Names         
#>  5 Run_Parameters   barcode_drug_plate
#>  6 Run_Parameters   user              
#>  7 Run_Parameters   Plate_Size        
#>  8 Run_Parameters   Plate_Type        
#>  9 Run_Parameters   Samples_to_Run    
#> 10 Run_Parameters   Overlay_Size      
#> # … with 2,969 more rows