datacarpentry/shell-genomics

Suggestion for Adding `cut` to "Writing Scripts and Working with Data"

dr-aheydari opened this issue · 6 comments

dr-aheydari commented

Hello,

I think the content and the organization of the lesson is great, but I was wondering if there could be a short section on using cut in addition to grep. I believe this would further enhance the learning of the data carpentry learners since using cut can help with easier manipulation of data that have fields (or columns), which one could expect from many datasets (with standard formats). Adding this section should not make the learning experience much harder, but it would provide another valuable tool to the beginners' repertoire.

Thank you for considering this suggestion.

akshayparopkari commented

Hi @dr-aheydari, thanks for raising this issue.

grep is introduced in episode 4. Redirection. I do agree with you that cut is utilized in combination with grep for tabular data (e.g. CSV, TSV, tab, etc.). I think, when teaching this lesson, the instructor may verbally communicate grep + cut pipe combination as an independent example to highlight the versatility of bash commands.

Thoughts / inputs, @datacarpentry/shell-genomics-maintainers?

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aschuerch commented

There is a lesson on cut and grep (See https://datacarpentry.org/shell-genomics/Extra_lesson/index.html). This used to be part of the core lessons but was moved to Extras to make some room in this lesson (as it can be difficult to teach fully in the 4 hours). Does this lesson cover what you suggested?

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akshayparopkari commented

Thanks @aschuerch 👍

I wasn't aware of the extra lesson on file manipulation. I'm happy to be learning new things about this lesson. Also, I have been wondering about the inclusion of shell_data/sra_metadata/SraRunTable.txt was included in the lesson since it isn't referenced in any episodes. I see that it is used in the extra lesson ✅

aschuerch commented

@akshayparopkari I think embedding of the extra content could be improved. Have a look at pull request #273 for an extra callout to point instructors and/or self-guided learners to the extra material. I've put the callout where the material used to be.

dr-aheydari commented

@aschuerch Thank you very much for pointing me to the "Extra Lesson" section. I understand why it would be hard to include cut and grep in the lesson and cover all the material. Thank you for your explanation.

aschuerch commented

Thanks for the feedback @dr-aheydari, I am closing this issue now.