dirdf - Extracts Metadata from Directory and File Names
Create tidy data frames of file metadata from directory and file names.
Install
This package is only available on GitHub - it is not available on CRAN. Install it as:
remotes::install_github("ropenscilabs/dirdf")Examples
path <- system.file("examples", "dataset_1", package = "dirdf")
dir(path)## [1] "2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A01.csv"
## [2] "2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A02.csv"
## [3] "2014-02-26_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41_D08.csv"
## [4] "2014-03-05_BRAFWTNEGASSAY_FFPEDNA-CRC-REPEAT_platefile.csv"
## [5] "2016-04-01_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41.csv"
dirdf::dirdf(path, template = "Date_Assay_Plasmid-Type-Fraction_WellNumber?.extension")## Date Assay Plasmid Type Fraction
## 1 2013-06-26 BRAFWTNEGASSAY Plasmid Cellline 100-1MutantFraction
## 2 2013-06-26 BRAFWTNEGASSAY Plasmid Cellline 100-1MutantFraction
## 3 2014-02-26 BRAFWTNEGASSAY FFPEDNA CRC 1-41
## 4 2014-03-05 BRAFWTNEGASSAY FFPEDNA CRC REPEAT
## 5 2016-04-01 BRAFWTNEGASSAY FFPEDNA CRC 1-41
## WellNumber extension
## 1 A01 csv
## 2 A02 csv
## 3 D08 csv
## 4 platefile csv
## 5 <NA> csv
## pathname
## 1 2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A01.csv
## 2 2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A02.csv
## 3 2014-02-26_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41_D08.csv
## 4 2014-03-05_BRAFWTNEGASSAY_FFPEDNA-CRC-REPEAT_platefile.csv
## 5 2016-04-01_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41.csv
dirdf::dirdf(path, template = "Year-Month-Day_Assay_Plasmid-Type-Fraction_WellNumber?.extension")## Year Month Day Assay Plasmid Type Fraction
## 1 2013 06 26 BRAFWTNEGASSAY Plasmid Cellline 100-1MutantFraction
## 2 2013 06 26 BRAFWTNEGASSAY Plasmid Cellline 100-1MutantFraction
## 3 2014 02 26 BRAFWTNEGASSAY FFPEDNA CRC 1-41
## 4 2014 03 05 BRAFWTNEGASSAY FFPEDNA CRC REPEAT
## 5 2016 04 01 BRAFWTNEGASSAY FFPEDNA CRC 1-41
## WellNumber extension
## 1 A01 csv
## 2 A02 csv
## 3 D08 csv
## 4 platefile csv
## 5 <NA> csv
## pathname
## 1 2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A01.csv
## 2 2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A02.csv
## 3 2014-02-26_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41_D08.csv
## 4 2014-03-05_BRAFWTNEGASSAY_FFPEDNA-CRC-REPEAT_platefile.csv
## 5 2016-04-01_BRAFWTNEGASSAY_FFPEDNA-CRC-1-41.csv
Inconsistent file names
path <- system.file("examples", "dataset_2", package = "dirdf")
dir(path)## [1] "2011-12-16_OTHERASSAY_FFPEDNA-CRC-1-41_D08.csv"
## [2] "2013-06-26_OTHERASSAY_Plasmid-Cellline-100-1MutantFraction_B02.csv"
## [3] "2014-03-05_OTHERASSAY_FFPEDNA-CRC-REPEAT_platefile.csv"
## [4] "2014-07-06_OTHERASSAY_Plasmid-Cellline-100-1MutantFraction_B01.csv"
## [5] "2016-01-11_OTHERASSAY_FFPEDNA-CRC-2-41.csv"
dirdf::dirdf(path, template = "date_assay_experiment_well.ext")## Error in dirdf_parse(pathnames, template = template, colnames = colnames, : Unexpected path(s) found:
## 2016-01-11_OTHERASSAY_FFPEDNA-CRC-2-41.csv
dirdf::dirdf(path, template = "date_assay_experiment_well?.ext")## date assay experiment well ext
## 1 2011-12-16 OTHERASSAY FFPEDNA-CRC-1-41 D08 csv
## 2 2013-06-26 OTHERASSAY Plasmid-Cellline-100-1MutantFraction B02 csv
## 3 2014-03-05 OTHERASSAY FFPEDNA-CRC-REPEAT platefile csv
## 4 2014-07-06 OTHERASSAY Plasmid-Cellline-100-1MutantFraction B01 csv
## 5 2016-01-11 OTHERASSAY FFPEDNA-CRC-2-41 <NA> csv
## pathname
## 1 2011-12-16_OTHERASSAY_FFPEDNA-CRC-1-41_D08.csv
## 2 2013-06-26_OTHERASSAY_Plasmid-Cellline-100-1MutantFraction_B02.csv
## 3 2014-03-05_OTHERASSAY_FFPEDNA-CRC-REPEAT_platefile.csv
## 4 2014-07-06_OTHERASSAY_Plasmid-Cellline-100-1MutantFraction_B01.csv
## 5 2016-01-11_OTHERASSAY_FFPEDNA-CRC-2-41.csv
Metadata in directory and path names
> dir("examples/", recursive = TRUE)
[1] "LabA,2016/2013-06-26_BRAFWTNEG_Plasmid-Cellline-100_A01.csv"
[2] "LabA,2016/2013-06-26_BRAFWTNEG_Plasmid-Cellline-100_A02.csv"
[3] "LabA,2016/2014-02-26_BRAFWTNEG_FFPEDNA-CRC-1-41_D08.csv"
[4] "LabA,2016/2014-03-05_BRAFWTNEG_FFPEDNA-CRC-REPEAT_H03.csv"
[5] "LabA,2016/2016-04-01_BRAFWTNEG_FFPEDNA-CRC-1-41_E12.csv"
[6] "LabB,2015/2011-12-16_OTHER_FFPEDNA-CRC-1-41_D08.csv"
[7] "LabB,2015/2013-06-26_OTHER_Plasmid-Cellline-100_B02.csv"
[8] "LabB,2015/2014-03-05_OTHER_FFPEDNA-CRC-REPEAT_H03.csv"
[9] "LabB,2015/2014-07-06_OTHER_Plasmid-Cellline-100_B01.csv"
[10] "LabB,2015/2016-01-11_OTHER_FFPEDNA-CRC-2-41.csv"
> dirdf::dirdf("examples/", template = "lab,year/date_assay_experiment_well?.ext")
lab year date assay experiment well ext pathname
1 LabA 2016 2013-06-26 BRAFWTNEG Plasmid-Cellline-100 A01 csv LabA,2016/2013-06-26_BRAFWTNEG_Plasmid-Cellline-100_A01.csv
2 LabA 2016 2013-06-26 BRAFWTNEG Plasmid-Cellline-100 A02 csv LabA,2016/2013-06-26_BRAFWTNEG_Plasmid-Cellline-100_A02.csv
3 LabA 2016 2014-02-26 BRAFWTNEG FFPEDNA-CRC-1-41 D08 csv LabA,2016/2014-02-26_BRAFWTNEG_FFPEDNA-CRC-1-41_D08.csv
4 LabA 2016 2014-03-05 BRAFWTNEG FFPEDNA-CRC-REPEAT H03 csv LabA,2016/2014-03-05_BRAFWTNEG_FFPEDNA-CRC-REPEAT_H03.csv
5 LabA 2016 2016-04-01 BRAFWTNEG FFPEDNA-CRC-1-41 E12 csv LabA,2016/2016-04-01_BRAFWTNEG_FFPEDNA-CRC-1-41_E12.csv
6 LabB 2015 2011-12-16 OTHER FFPEDNA-CRC-1-41 D08 csv LabB,2015/2011-12-16_OTHER_FFPEDNA-CRC-1-41_D08.csv
7 LabB 2015 2013-06-26 OTHER Plasmid-Cellline-100 B02 csv LabB,2015/2013-06-26_OTHER_Plasmid-Cellline-100_B02.csv
8 LabB 2015 2014-03-05 OTHER FFPEDNA-CRC-REPEAT H03 csv LabB,2015/2014-03-05_OTHER_FFPEDNA-CRC-REPEAT_H03.csv
9 LabB 2015 2014-07-06 OTHER Plasmid-Cellline-100 B01 csv LabB,2015/2014-07-06_OTHER_Plasmid-Cellline-100_B01.csv
10 LabB 2015 2016-01-11 OTHER FFPEDNA-CRC-2-41 <NA> csv LabB,2015/2016-01-11_OTHER_FFPEDNA-CRC-2-41.csv