How to name files

Transcript

1. naming things
   prepared by Jenny Bryan for
   Reproducible Science Workshop
   

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2. Names matter
   

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3. myabstract.docx
   Joe’s Filenames Use Spaces and Punctuation.xlsx
   figure 1.png
   fig 2.png
   JW7d^(2sl@deletethisandyourcareerisoverWx2*.txt
   NO
   2014-06-08_abstract-for-sla.docx
   joes-filenames-are-getting-better.xlsx
   fig01_scatterplot-talk-length-vs-interest.png
   fig02_histogram-talk-attendance.png
   1986-01-28_raw-data-from-challenger-o-rings.txt
   YES
   

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4. machine readable
   human readable
   plays well with default ordering
   three principles for (file) names
   

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5. awesome file names :)
   

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6. “machine readable”
   regular expression and globbing friendly
   - avoid spaces, punctuation, accented
   characters, case sensitivity
   easy to compute on
   - deliberate use of delimiters
   

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7. Jennifers-MacBook-Pro-3:2014-03-21 jenny$ ls *Plasmid*
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A01.csv
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A02.csv
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A03.csv
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_B01.csv
   ....
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_H03.csv
   2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_platefile.csv
   Excerpt of complete file listing:
   Example of globbing to narrow file listing:
   

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8. Same using Mac OS Finder search facilities:
   

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9. Same using R’s ability to narrow file list by regex:
   > list.files(pattern = "Plasmid") %>% head
   [1] "2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A01.csv"
   [2] "2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A02.csv"
   [3] "2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_A03.csv"
   [4] "2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_B01.csv"
   [5] "2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_B02.csv"
   [6] "2013-06-26_BRAFWTNEGASSAY_Plasmid-Cellline-100-1MutantFraction_B03.csv"
   

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10. Deliberate use of “_” and “-” allows us to recover meta-
    data from the filenames.
    > flist <- list.files(pattern = "Plasmid") %>% head
    > stringr::str_split_fixed(flist, "[_\\.]", 5)
    [,1] [,2] [,3] [,4] [,5]
    [1,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "A01" "csv"
    [2,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "A02" "csv"
    [3,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "A03" "csv"
    [4,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "B01" "csv"
    [5,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "B02" "csv"
    [6,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "B03" "csv"
    This happens to be R but also possible in the shell, Python, etc.
    date assay sample set well
    

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11. > flist <- list.files(pattern = "Plasmid") %>% head
    > stringr::str_split_fixed(flist, "[_\\.]", 5)
    [,1] [,2] [,3] [,4] [,5]
    [1,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "A01" "csv"
    [2,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "A02" "csv"
    [3,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "A03" "csv"
    [4,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "B01" "csv"
    [5,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "B02" "csv"
    [6,] "2013-06-26" "BRAFWTNEGASSAY" "Plasmid-Cellline-100-1MutantFraction" "B03" "csv"
    “_” underscore used to delimit units of meta-data I want later
    “-” hyphen used to delimit words so my eyes don’t bleed
    

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12. easy to search for files later
    easy to narrow file lists based on names
    easy to extract info from file names, e.g. by splitting
    new to regular expressions and globbing? be kind to
    yourself and avoid
    - spaces in file names
    - punctuation
    - accented characters
    - different files named “foo” and “Foo”
    “machine readable”
    

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13. “human readable”
    name contains info on content
    connects to concept of a slug from
    semantic URLs
    

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14. “human readable”
    Jennifers-MacBook-Pro-3:analysis jenny$ ls -1
    01_marshal-data.md
    01_marshal-data.r
    02_pre-dea-filtering.md
    02_pre-dea-filtering.r
    03_dea-with-limma-voom.md
    03_dea-with-limma-voom.r
    04_explore-dea-results.md
    04_explore-dea-results.r
    90_limma-model-term-name-fiasco.md
    90_limma-model-term-name-fiasco.r
    Makefile
    figure
    helper01_load-counts.r
    helper02_load-exp-des.r
    helper03_load-focus-statinf.r
    helper04_extract-and-tidy.r
    tmp.txt
    01.md
    01.r
    02.md
    02.r
    03.md
    03.r
    04.md
    04.r
    90.md
    90.r
    Makefile
    figure
    helper01.r
    helper02.r
    helper03.r
    helper04.r
    tmp.txt
    Which set of file(name)s do you want at 3a.m. before a deadline?
    

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15. “human readable”
    embrace the slug
    01_marshal-data.r
    02_pre-dea-filtering.r
    03_dea-with-limma-voom.r
    04_explore-dea-results.r
    90_limma-model-term-name-fiasco.r
    helper01_load-counts.r
    helper02_load-exp-des.r
    helper03_load-focus-statinf.r
    helper04_extract-and-tidy.r
    

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16. “human readable”
    easy to figure out what the heck
    something is, based on its name
    

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17. “plays well with default ordering”
    put something numeric first
    use the ISO 8601 standard for dates
    left pad other numbers with zeros
    

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18. “plays well with default ordering”
    01_marshal-data.r
    02_pre-dea-filtering.r
    03_dea-with-limma-voom.r
    04_explore-dea-results.r
    90_limma-model-term-name-fiasco.r
    helper01_load-counts.r
    helper02_load-exp-des.r
    helper03_load-focus-statinf.r
    helper04_extract-and-tidy.r
    chronological
    order
    logical
    order
    

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19. “plays well with default ordering”
    01_marshal-data.r
    02_pre-dea-filtering.r
    03_dea-with-limma-voom.r
    04_explore-dea-results.r
    90_limma-model-term-name-fiasco.r
    helper01_load-counts.r
    helper02_load-exp-des.r
    helper03_load-focus-statinf.r
    helper04_extract-and-tidy.r
    put something numeric first
    

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20. “plays well with default ordering”
    use the ISO 8601 standard for dates
    YYYY-MM-DD
    

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21. http://xkcd.com/1179/
    

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22. Comprehensive map of all countries in the
    world that use the MMDDYYYY format
    https://twitter.com/donohoe/status/597876118688026624
    

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23. left pad other numbers with zeros
    01_marshal-data.r
    02_pre-dea-filtering.r
    03_dea-with-limma-voom.r
    04_explore-dea-results.r
    90_limma-model-term-name-fiasco.r
    helper01_load-counts.r
    helper02_load-exp-des.r
    helper03_load-focus-statinf.r
    helper04_extract-and-tidy.r
    if you don’t left pad, you get this:
    10_final-figs-for-publication.R
    1_data-cleaning.R
    2_fit-model.R
    which is just sad
    

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24. “plays well with default ordering”
    put something numeric first
    use the ISO 8601 standard for dates
    left pad other numbers with zeros
    

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25. machine readable
    human readable
    plays well with default ordering
    three principles for (file) names
    

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26. easy to implement NOW
    payoffs accumulate as your skills evolve
    and projects get more complex
    three principles for (file) names
    

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27. go forth and use awesome file names :)
    01_marshal-data.r
    02_pre-dea-filtering.r
    03_dea-with-limma-voom.r
    04_explore-dea-results.r
    90_limma-model-term-name-fiasco.r
    helper01_load-counts.r
    helper02_load-exp-des.r
    helper03_load-focus-statinf.r
    helper04_extract-and-tidy.r
    

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