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fix link to regex resource and update pt 2 slides
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Natalie Elphick
parent
da9e3819db
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4 changed files with 32 additions and 34 deletions
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@ -2266,9 +2266,9 @@ macOS 14.1 January 9, 2021 macOS 14.1</code></pre>
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data</li>
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<li><strong>Strings</strong> : sequence of characters</li>
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</ul>
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<pre class="text"><code>message="Hello, World!"
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<pre class="text"><code>message="Hello, World"
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echo $message</code></pre>
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<pre><code>Hello, World!</code></pre>
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<pre><code>Hello, World</code></pre>
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<p>Here, we assign the string “Hello, World!” to the variable
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<code>message</code> and use echo to print its value.</p>
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</section>
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@ -2351,8 +2351,8 @@ size)</li>
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</ul>
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<pre class="text"><code>ls -lah part_1</code></pre>
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<pre><code>total 8
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drwx---rw-@ 4 nelphick staff 128B Mar 11 10:11 .
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drwxr-xr-x@ 5 nelphick staff 160B Mar 11 10:11 ..
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drwx---rw-@ 4 nelphick staff 128B Mar 12 09:18 .
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drwxr-xr-x@ 5 nelphick staff 160B Mar 12 09:27 ..
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-rw-r--r--@ 1 nelphick staff 0B Apr 11 2023 .hidden_file.txt
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-rw-r--r--@ 1 nelphick staff 60B Apr 12 2023 list_numbers.tsv</code></pre>
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</section>
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@ -2365,8 +2365,8 @@ ls -l</code></pre>
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<pre><code>cd ..
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ls -l</code></pre>
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<pre><code>total 0
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drwx---rw-@ 4 nelphick staff 128 Mar 11 10:11 part_1
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drwxr-xr-x@ 3 nelphick staff 96 Mar 11 10:11 part_2</code></pre>
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drwx---rw-@ 4 nelphick staff 128 Mar 12 09:18 part_1
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drwxr-xr-x@ 3 nelphick staff 96 Mar 12 09:27 part_2</code></pre>
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</section></section>
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<section>
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<section id="creating-and-altering-files" class="title-slide slide level1">
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@ -2441,7 +2441,9 @@ used on <strong>cannot be recovered</strong></li>
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<pre class="text"><code>du -h */*</code></pre>
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<pre><code> 0B new_directory/new_file1.txt
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4.0K part_1/list_numbers.tsv</code></pre>
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<p>-h - Displays the output in human readable format</p>
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<ul>
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<li>h - Displays the output in human readable format</li>
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</ul>
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</section>
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<section id="check-in" class="slide level2">
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<h2>Check-in</h2>
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@ -2573,7 +2575,7 @@ directory</li>
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<section id="regular-expressions" class="slide level2">
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<h2>Regular Expressions</h2>
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<ul>
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<li>For a more extensive overview of regular expressions click <a href="https://v4.software-carpentry.org/regexp/index.html">here</a></li>
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<li>For a more extensive overview of regular expressions click <a href="https://regexone.com/lesson/introduction_abcs">here</a></li>
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<li>Some basic ones are:
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<ul>
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<li>” ^ ” Matches the beginning of a line</li>
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@ -1932,7 +1932,7 @@ files and/or folders that have been compressed</p>
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du -h part_2/homo_sapiens.refseq.tsv</code></pre>
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<pre><code> 33M part_2/homo_sapiens.refseq.tsv</code></pre>
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<ul>
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<li>The uncompressed file is 27 megabytes</li>
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<li>The uncompressed file is 33 megabytes</li>
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</ul>
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<pre class="text"><code>gzip part_2/homo_sapiens.refseq.tsv
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du -h part_2/homo_sapiens.refseq.tsv.gz</code></pre>
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@ -1961,9 +1961,9 @@ compressed archive files</li>
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<pre class="text"><code>tar -czf part_1.tar.gz part_1
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ls -l</code></pre>
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<pre><code>total 8
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drwx---rw-@ 4 nelphick staff 128 Mar 11 10:11 part_1
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-rw-r--r--@ 1 nelphick staff 800 Mar 11 10:11 part_1.tar.gz
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drwxr-xr-x@ 4 nelphick staff 128 Mar 11 10:11 part_2</code></pre>
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drwx---rw-@ 4 nelphick staff 128 Mar 12 09:36 part_1
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-rw-r--r-- 1 nelphick staff 803 Mar 12 10:00 part_1.tar.gz
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drwxr-xr-x@ 4 nelphick staff 128 Mar 12 10:00 part_2</code></pre>
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<ul>
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<li>-c: create a new archive</li>
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<li>-f: specify the name of the archive file</li>
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@ -2024,8 +2024,11 @@ system’s state</li>
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<li><strong>$PWD</strong> : The working directory</li>
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<li><strong>$HOME</strong> : The current user’s home directory</li>
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<li><strong>$PS1</strong> : the shell prompt string</li>
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<li><strong>$TEMP</strong> : location of temporary files</li>
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<li><strong>$TMPDIR</strong> : location of temporary files</li>
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</ul>
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<p>These can change depending on the specific OS or program,
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<strong>TMPDIR</strong> can also be <strong>TEMP</strong>,
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<strong>TEMPDIR</strong> and <strong>TMP</strong>.</p>
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</section>
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<section id="path-locations-of-executable-files" class="slide level2">
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<h2>PATH: locations of executable files</h2>
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@ -2106,13 +2109,13 @@ interpreter is</li>
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<li>By default, files are not executable</li>
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</ul>
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<pre class="text"><code>ls -l part_2/example_script.sh</code></pre>
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<pre><code>-rw-r--r--@ 1 nelphick staff 287 Mar 11 10:11 part_2/example_script.sh</code></pre>
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<pre><code>-rw-r--r-- 1 nelphick staff 287 Mar 12 10:00 part_2/example_script.sh</code></pre>
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<ul>
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<li>We can set the execute bit like this</li>
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</ul>
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<pre class="text"><code>chmod u+x part_2/example_script.sh
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ls -l part_2/example_script.sh</code></pre>
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<pre><code>-rwxr--r--@ 1 nelphick staff 287 Mar 11 10:11 part_2/example_script.sh</code></pre>
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<pre><code>-rwxr--r-- 1 nelphick staff 287 Mar 12 10:00 part_2/example_script.sh</code></pre>
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</section>
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<section id="example" class="slide level2">
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<h2>Example</h2>
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@ -2188,7 +2191,7 @@ fi # end if statement</code></pre>
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language</li>
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<li>It reads and modifies text line by line from a file or input
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stream</li>
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<li>Supports <a href="https://v4.software-carpentry.org/regexp/index.html">regular
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<li>Supports <a href="https://regexone.com/lesson/introduction_abcs">regular
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expressions</a></li>
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<li>Useful for replacing text</li>
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</ul>
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@ -2283,12 +2286,6 @@ Bruce Barnett</a></li>
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<section id="end-of-part-2" class="title-slide slide level1">
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<h1>End of Part 2</h1>
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</section>
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<section id="survey" class="slide level2">
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<h2>Survey</h2>
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<ul>
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<li>Please take some time to fill out the workshop survey: <a href="https://www.surveymonkey.com/r/DY7K5ZY" class="uri">https://www.surveymonkey.com/r/DY7K5ZY</a></li>
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</ul>
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</section>
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<section id="additional-learning-materials" class="slide level2">
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<h2>Additional learning materials</h2>
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@ -2307,11 +2304,11 @@ Line</a></li>
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</ul></li>
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</ul>
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</section>
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<section id="survey-1" class="slide level2">
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<section id="survey" class="slide level2">
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<h2>Survey</h2>
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<ul>
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<li>Please take some time to fill out the workshop survey:<br />
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<a href="https://www.surveymonkey.com/r/F75J6VZ" class="uri">https://www.surveymonkey.com/r/F75J6VZ</a></li>
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<a href="https://www.surveymonkey.com/r/DY7K5ZY" class="uri">https://www.surveymonkey.com/r/DY7K5ZY</a></li>
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</ul>
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</section>
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<section id="upcoming-data-science-training-program-workshops" class="slide level2">
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@ -163,7 +163,7 @@ man -P cat man | col -b
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- **Variables** : a named container that holds a value or data
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- **Strings** : sequence of characters
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```{r, engine='bash', eval=TRUE, results='markup', highlight=FALSE, comment=NA, echo = TRUE}
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message="Hello, World!"
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message="Hello, World"
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echo $message
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```
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@ -347,7 +347,7 @@ rm new_directory/new_file2.txt
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```{r, engine='bash', eval=TRUE, results='markup', highlight=FALSE, comment=NA}
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du -h */*
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```
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-h - Displays the output in human readable format
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- h - Displays the output in human readable format
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## Check-in
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@ -447,7 +447,7 @@ grep "7" part_1/list_numbers.tsv
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## Regular Expressions
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- For a more extensive overview of regular expressions click [here](https://v4.software-carpentry.org/regexp/index.html)
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- For a more extensive overview of regular expressions click [here](https://regexone.com/lesson/introduction_abcs)
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- Some basic ones are:
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- " ^ " Matches the beginning of a line
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- " . " Matches any single character except newline
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@ -89,7 +89,7 @@ gunzip part_2/homo_sapiens.refseq.tsv.gz
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du -h part_2/homo_sapiens.refseq.tsv
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```
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- The uncompressed file is 27 megabytes
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- The uncompressed file is 33 megabytes
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```{r, engine='bash', eval=TRUE, results='markup', highlight=FALSE, comment=NA, echo = TRUE}
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gzip part_2/homo_sapiens.refseq.tsv
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@ -162,7 +162,9 @@ echo $HOME
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- **$PWD** : The working directory
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- **$HOME** : The current user's home directory
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- **$PS1** : the shell prompt string
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- **$TEMP** : location of temporary files
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- **$TMPDIR** : location of temporary files
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These can change depending on the specific OS or program, **TMPDIR** can also be **TEMP**, **TEMPDIR** and **TMP**.
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@ -309,7 +311,7 @@ fi # end if statement
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- Parses and transforms text, using a compact programming language
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- It reads and modifies text line by line from a file or input stream
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- Supports [regular expressions](https://v4.software-carpentry.org/regexp/index.html)
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- Supports [regular expressions](https://regexone.com/lesson/introduction_abcs)
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- Useful for replacing text
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Example:
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@ -394,10 +396,7 @@ END {print sum / count}'
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## Survey
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- Please take some time to fill out the workshop survey:
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https://www.surveymonkey.com/r/DY7K5ZY
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## Additional learning materials
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@ -412,7 +411,7 @@ https://www.surveymonkey.com/r/DY7K5ZY
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## Survey
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- Please take some time to fill out the workshop survey:
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https://www.surveymonkey.com/r/F75J6VZ
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https://www.surveymonkey.com/r/DY7K5ZY
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## Upcoming Data Science Training Program Workshops
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