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GUI (graphical user interface): easy but not reproducible.
CLI (command line interface) or REPL (read-evaluate-print loop): steep learning curve but reproducible and powerful.
The shell is an incredibly powerful tool:

• Gary Bernhardt: Unix is like a chainsaw. Can kill trees, and people. The Unix shell can do great things, but power comes with danger: it’s unsafe!
• example:

$ rm -rf tmp-data/aligned-reads*

deletes all large alignment files aligned-reads_1 to aligned-reads_1000 in old temporary directory tmp-data.

rm is to remove files & directories
-r will do it recursively (enter each directory within each directory)
-f will “force” removal without asking you confirmation for each individual file
* in the shell will match anything

with unintended extra space:

$ rm -rf tmp-data/aligned-reads *
rm: tmp-data/aligned-reads: No such file or directory

deletes your entire current directory (ouch!)

Later in the semester, watch the shell script example from Gary Bernhardt’s talk at 16:21-18:40 : you should understand exactly how it does what it does.

modularity

This is the Unix philosophy: Write programs that do one thing and do it well.
Write programs to work together. Write programs to handle text streams,
because that is a universal interface.
—- Doug McIlory

• modularity
• pipes: STDIN –> myprogram –> STDOUT

Advantages to modularity:

• easier to spot errors, and fix them
• experiments with alternative choices at one step in the pipeline
• choose appropriate tool for each step, e.g. C++ -> Python -> R
• modules possible reusable for other tasks later on

text streams

to process a stream of data rather than holding it all in memory.

Example: concatenate two data files. Open both in editor, copy one and paste into the other?

• may not have enough memory
• manual operation: error-prone and not reproducible.

Instead: print the files’s content to standard output stream and redirect this stream from our terminal to the file we wish to save the combined results to.

cd bds-files/chapter-03-remedial-unix/
cat tb1-protein.fasta
cat tga1-protein.fasta
cat tb1-protein.fasta tga1-protein.fasta
cat tb1-protein.fasta tga1-protein.fasta > zea-proteins.fasta
ls -lrt

-l: in list format
-r: in reverse order
-t: ordered by time

Streams process data without storing huge amounts in our computers’ memory: very efficient

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