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https://github.com/henrikbengtsson/dirdf

R package: dirdf - Extracts Metadata from Directory and File Names
https://github.com/henrikbengtsson/dirdf

files metadata package r r-package rstats unconf unconf16

Last synced: 29 days ago
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R package: dirdf - Extracts Metadata from Directory and File Names

Host: GitHub
URL: https://github.com/henrikbengtsson/dirdf
Owner: HenrikBengtsson
License: other
Created: 2016-04-01T17:59:56.000Z (almost 9 years ago)
Default Branch: master
Last Pushed: 2021-03-25T22:27:46.000Z (almost 4 years ago)
Last Synced: 2024-12-04T09:40:06.197Z (about 1 month ago)
Topics: files, metadata, package, r, r-package, rstats, unconf, unconf16
Language: R
Homepage: https://github.com/HenrikBengtsson/dirdf
Size: 67.4 KB
Stars: 58
Watchers: 13
Forks: 1
Open Issues: 3
Metadata Files:
- Readme: README.md
- Changelog: NEWS
- License: LICENSE

Awesome Lists containing this project

README

# dirdf - Extracts Metadata from Directory and File Names

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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:
```r
remotes::install_github("ropenscilabs/dirdf")
```

## Examples

``` r
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"

``` r
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 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

``` r
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 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
-----------------------

``` r
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"

``` r
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

``` r
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 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
------------------------------------

``` r
> 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
```

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