Moved exercises into subfolders of the corresponding topics

JJiao · Mar 4, 2013 · 39e0701 · 39e0701
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diff --git a/exercises/setdict.markdown → ...ata_structures/exercises/setdict.markdown b/exercises/setdict.markdown → ...ata_structures/exercises/setdict.markdown
diff --git a/exercises/setdict_dependencies.txt → ...ctures/exercises/setdict_dependencies.txt b/exercises/setdict_dependencies.txt → ...ctures/exercises/setdict_dependencies.txt
diff --git a/exercises/python.markdown → python/intro/exercises/python.markdown b/exercises/python.markdown → python/intro/exercises/python.markdown
diff --git a/exercises/oop.markdown → ...on/obj_orientation/exercises/oop.markdown b/exercises/oop.markdown → ...on/obj_orientation/exercises/oop.markdown
diff --git a/exercises/oop_sushi.txt → ...n/obj_orientation/exercises/oop_sushi.txt b/exercises/oop_sushi.txt → ...n/obj_orientation/exercises/oop_sushi.txt
diff --git a/exercises/regexp.markdown → python/regexp/exercises/regexp.markdown b/exercises/regexp.markdown → python/regexp/exercises/regexp.markdown
diff --git a/exercises/invperc.markdown → python/sw_engineering/argparse_exercise.md b/exercises/invperc.markdown → python/sw_engineering/argparse_exercise.md
@@ -1,5 +1,3 @@
-
-
 ## Exercise 1
 
 In the episode on [Randomness](http://software-carpentry.org/4_0/invperc/random)

diff --git a/exercises/test.markdown → python/testing/exercises/test.markdown b/exercises/test.markdown → python/testing/exercises/test.markdown
diff --git a/exercises/shell_1000gp.vcf → shell/exercises/1000gp.vcf b/exercises/shell_1000gp.vcf → shell/exercises/1000gp.vcf
diff --git a/exercises/shell.markdown → shell/exercises/shell.markdown b/exercises/shell.markdown → shell/exercises/shell.markdown
@@ -2,7 +2,7 @@
 
 Let's try out your new shell skills on some real data.
 
-The file `shell_1000gp.vcf` is a small sample (1%) of a very large text file
+The file `1000gp.vcf` is a small sample (1%) of a very large text file
 containing human genetics data. Specifically, it describes genetic variation in
 three African individuals sequenced as part of the [1000 Genomes
 Project](http://www.1000genomes.org). 
@@ -16,7 +16,7 @@ path of all files with that name on the computer (using the shell)?
   > `$ man find`
 
   **Answer:**
-  > `$ find / -name "shell_1000gp.vcf"`
+  > `$ find / -name "1000gp.vcf"`
 
 * It's usually a good idea to use an empty directory as a workspace so that
   other files don't get in the way (or accidentally get overwritten or deleted).
@@ -28,7 +28,7 @@ path of all files with that name on the computer (using the shell)?
   **Answer:**
   > ```bash
   > $ mkdir sandbox
-  > $ mv /home/orion/Downloads/shell_1000gp.vcf sandbox
+  > $ mv /home/orion/Downloads/1000gp.vcf sandbox
   > $ cd sandbox
   > ```
 
@@ -68,12 +68,12 @@ path of all files with that name on the computer (using the shell)?
 
   **Answer:**
   > We should get a file size around 3.6 MB with:
-  > `$ ls -lh shell_1000gp.vcf`
+  > `$ ls -lh 1000gp.vcf`
   > Alternatively, the command `du` can be used to achieve a similar result:
-  > `$ du -h shell_1000gp.vcf`
+  > `$ du -h 1000gp.vcf`
   > 
   > We find there are 45034 lines with:
-  > `$ wc -l shell_1000gp.vcf`
+  > `$ wc -l 1000gp.vcf`
 
 
 * Because this file is so large, you're going to almost always want to pipe
@@ -84,14 +84,14 @@ print 45,000 lines to the screen.
   Let's start by printing the first 5 lines to see what it looks like.  
 
   **Answer:**
-  > `$ head -5 shell_1000gp.vcf`
+  > `$ head -5 1000gp.vcf`
 
 * That isn't very interesting; it's just a bunch of the comments at the
 beginning of the file (they all start with "#")! Print the first 20 lines to see
 more of the file.
 
   **Answer:**
-  > `$ head -20 shell_1000gp.vcf`
+  > `$ head -20 1000gp.vcf`
 
 
 * Okay, so now we can see the basic structure of the file. A few comment lines
@@ -127,11 +127,11 @@ more of the file.
     $ grep -v "^$" file
 
   **Our answer:**
-  >     $ grep -v "^#" shell_1000gp.vcf | head
+  >     $ grep -v "^#" 1000gp.vcf | head
   > 
   > Why are neither of these correct?
-  >     $ grep -v "#" shell_1000gp.vcf | head
-  >     $ grep -v "^##" shell_1000gp.vcf | head
+  >     $ grep -v "#" 1000gp.vcf | head
+  >     $ grep -v "^##" 1000gp.vcf | head
 
 * How many lines of data are in the file (rather than counting the number of
   header lines and subtracting, try just counting the number of data lines)?
@@ -140,7 +140,7 @@ more of the file.
   > Instead of piping to `head`, try piping to `wc`.
 
   **Our Answer:**
-  >     $ grep -v "^#" shell_1000gp.vcf | wc -l
+  >     $ grep -v "^#" 1000gp.vcf | wc -l
   >
   > should print `45024`
 
@@ -159,7 +159,7 @@ more of the file.
   > chromosome column.
 
   **Our Answer:**
-  >     $ grep -v "^#" shell_1000gp.vcf | cut -f 1 | head
+  >     $ grep -v "^#" 1000gp.vcf | cut -f 1 | head
 
 * As you should have observed, the first 10 lines are on numbered chromosomes.
   Every normal cell in your body has 23 pairs of chromosomes, 22 pairs of
@@ -179,7 +179,7 @@ more of the file.
   > `sort` has an option that should make this easier.
 
   **Our Answer:**
-  >     $ grep -v "^#" shell_1000gp.vcf | cut -f 1 | sort -u
+  >     $ grep -v "^#" 1000gp.vcf | cut -f 1 | sort -u
 
 
 * Rather than using `sort` to print unique results, a common pipeline is to
@@ -199,7 +199,7 @@ more of the file.
   > the result to `uniq`.
 
   **Our Answer:**
-  >     $ grep -v "^#" shell_1000gp.vcf | cut -f 1 | sort | uniq -c
+  >     $ grep -v "^#" 1000gp.vcf | cut -f 1 | sort | uniq -c
 
 
 * Add to your previous solution to list the chromosomes from most frequently
@@ -213,7 +213,7 @@ more of the file.
   > ascending order.
 
   **Our Answer:**
-  >     $ grep -v "^#" shell_1000gp.vcf | cut -f 1 | sort | uniq -c | sort -n -r
+  >     $ grep -v "^#" 1000gp.vcf | cut -f 1 | sort | uniq -c | sort -n -r
   >
   > should output the following:
   >
@@ -276,12 +276,12 @@ more of the file.
   > only need to sort on one field.
 
   **Answer:**
-  >     $ grep -v "^#" shell_1000gp.vcf | cut -f 1 | sort | uniq -c | sort -k 2n
+  >     $ grep -v "^#" 1000gp.vcf | cut -f 1 | sort | uniq -c | sort -k 2n
 
 
 ## Exercise Part 3 (scripts and svn)
 * Wonderful! Now we have a (long) command for printing chromosome statistics
-  from our `shell_1000gp.vcf` file. Using `nano`, create a new file, "chrom_stats.sh",
+  from our `1000gp.vcf` file. Using `nano`, create a new file, "chrom_stats.sh",
   with just your answer to the previous question in it.
 
   **Answer:**
@@ -301,7 +301,7 @@ more of the file.
   > single-quotes or escape these with back-slashes.
 
   **Answer:**
-    $ echo 'grep -v "^#" shell_1000gp.vcf | cut -f 1 | sort | uniq -c | sort -k 2n' > chrom_stats.sh
+    $ echo 'grep -v "^#" 1000gp.vcf | cut -f 1 | sort | uniq -c | sort -k 2n' > chrom_stats.sh
     $ cat chrom_stats.sh
 
 * Now, execute your new script to print the chromosome statistics.
@@ -323,7 +323,7 @@ more of the file.
   > allow anyone to execute it.
 
 * We'd like to be able to use this script in the future with arbitrary VCF
-  files, instead of just our `shell_1000gp.vcf` file. Edit the script so that it takes
+  files, instead of just our `1000gp.vcf` file. Edit the script so that it takes
   VCF-formatted text input on stdin and prints out chromosome statistics on
   stdout. This is simpler than you might think.
 
@@ -332,15 +332,15 @@ more of the file.
 
   **Answer:**
   > Change
-  > `grep -v "^#" shell_1000gp.vcf | ...`
+  > `grep -v "^#" 1000gp.vcf | ...`
   > to
   > `grep -v "^#" | ...`
   > 
   > Since this is in a file instead of the shell prompt, we aren't showing the
   > "$" at the beginning of the line.
 
 * Now that we have a script that reads from stdin and prints to stdout, how do
-  we run it on the `shell_1000gp.vcf` file to get the same output as before?
+  we run it on the `1000gp.vcf` file to get the same output as before?
 
   **Hint:**
   > The `cat` command is used to print files to stdout.
@@ -354,7 +354,7 @@ more of the file.
   > `./chrom_stats.sh`.
 
   **Answer:**
-  `$ cat shell_1000gp.vcf | ./chrom_stats.sh`
+  `$ cat 1000gp.vcf | ./chrom_stats.sh`
 
 * Finally, add a copy of this file to your folder in the class SVN repository.
   1. `cp chrom_stats.sh /path/to/repo/participants/user/`

diff --git a/exercises/spreadsheets.markdown → spreadsheets/exercises/spreadsheets.markdown b/exercises/spreadsheets.markdown → spreadsheets/exercises/spreadsheets.markdown
diff --git a/exercises/spreadsheets_ex1.xls → spreadsheets/exercises/spreadsheets_ex1.xls b/exercises/spreadsheets_ex1.xls → spreadsheets/exercises/spreadsheets_ex1.xls
diff --git a/exercises/spreadsheets_ex2.xls → spreadsheets/exercises/spreadsheets_ex2.xls b/exercises/spreadsheets_ex2.xls → spreadsheets/exercises/spreadsheets_ex2.xls
diff --git a/exercises/spreadsheets_ex3.xls → spreadsheets/exercises/spreadsheets_ex3.xls b/exercises/spreadsheets_ex3.xls → spreadsheets/exercises/spreadsheets_ex3.xls
diff --git a/exercises/databases_aggregation.markdown → sql/exercises/aggregation.markdown b/exercises/databases_aggregation.markdown → sql/exercises/aggregation.markdown
@@ -1,7 +1,7 @@
 ## Getting Started
 
 In these exercises we will be using a database of that contains information
-about Nobel Prizes:  [databases_nobel_prizes.sqlite](databases_nobel_prizes.sqlite). 
+about Nobel Prizes:  [nobel_prizes.sqlite](nobel_prizes.sqlite). 
 
 ## The exercises
 

diff --git a/exercises/databases_experiments.sqlite → sql/exercises/experiments.sqlite b/exercises/databases_experiments.sqlite → sql/exercises/experiments.sqlite
diff --git a/exercises/databases_experiments_null.sqlite → sql/exercises/experiments_null.sqlite b/exercises/databases_experiments_null.sqlite → sql/exercises/experiments_null.sqlite
diff --git a/...s/databases_experiments_subqueries.sqlite → sql/exercises/experiments_subqueries.sqlite b/...s/databases_experiments_subqueries.sqlite → sql/exercises/experiments_subqueries.sqlite
diff --git a/exercises/databases_filter.markdown → sql/exercises/filter.markdown b/exercises/databases_filter.markdown → sql/exercises/filter.markdown
@@ -1,7 +1,7 @@
 ## Getting Started
 
 In these exercises we will be using a database of that contains information
-about Nobel Prizes: [databases_nobel_prizes.sqlite](databases_nobel_prizes.sqlite). 
+about Nobel Prizes: [nobel_prizes.sqlite](nobel_prizes.sqlite). 
 
 ## The exercises
 

diff --git a/exercises/databases.markdown → sql/exercises/intro.markdown b/exercises/databases.markdown → sql/exercises/intro.markdown
diff --git a/exercises/databases_join.markdown → sql/exercises/join.markdown b/exercises/databases_join.markdown → sql/exercises/join.markdown
@@ -1,7 +1,7 @@
 ## Getting Started
 
 In these exercises we will be using a database of that contains information
-about experiments: [databases_experiments.sqlite](databases_experiments.sqlite). 
+about experiments: [experiments.sqlite](experiments.sqlite). 
 
 ## The exercises
 

diff --git a/exercises/databases_nobel_prizes.sqlite → sql/exercises/nobel_prizes.sqlite b/exercises/databases_nobel_prizes.sqlite → sql/exercises/nobel_prizes.sqlite
diff --git a/exercises/databases_null.markdown → sql/exercises/null.markdown b/exercises/databases_null.markdown → sql/exercises/null.markdown
@@ -2,12 +2,12 @@
 
 
 In these exercises we will be using a database of that contains information
-about experiments: [databases_experiments_null.sqlite](databases_experiments_null.sqlite).
+about experiments: [experiments_null.sqlite](experiments_null.sqlite).
 
 ## The exercises
 
 The Experiments database is described in the [JOIN
-exercises](databases_join.markdown). In the version of the database given above,
+exercises](join.markdown). In the version of the database given above,
 some of the data in the tables is missing, which you'll have to take into
 account.
 

diff --git a/exercises/databases_select.markdown → sql/exercises/select.markdown b/exercises/databases_select.markdown → sql/exercises/select.markdown
@@ -1,7 +1,7 @@
 ## Getting Started
 
 In these exercises we will be using a database of that contains information
-about Nobel Prizes [databases_nobel_prizes.sqlite](databases_nobel_prizes.sqlite). 
+about Nobel Prizes [nobel_prizes.sqlite](nobel_prizes.sqlite). 
 
 This database only contains one table: `Nobel_Prizes`. 
 

diff --git a/exercises/databases_sort.markdown → sql/exercises/sort.markdown b/exercises/databases_sort.markdown → sql/exercises/sort.markdown
@@ -2,7 +2,7 @@
 
 
 In these exercises we will be using a database of that contains information
-about Nobel Prizes: [databases_nobel_prizes.sqlite](databases_nobel_prizes.sqlite). 
+about Nobel Prizes: [nobel_prizes.sqlite](nobel_prizes.sqlite). 
 
 ## The exercises
 

diff --git a/exercises/databases_subqueries.markdown → sql/exercises/subqueries.markdown b/exercises/databases_subqueries.markdown → sql/exercises/subqueries.markdown
@@ -1,7 +1,7 @@
 ## Getting Started
 
 In these exercises we will be using a database of that contains information
-about experiments:  [databases_experiments_subqueries.sqlite](databases_experiments_subqueries.sqlite). 
+about experiments:  [experiments_subqueries.sqlite](experiments_subqueries.sqlite). 
 
 
 ## The exercises

diff --git a/exercises/vc_exercise_4.cgi → version-control/svn/exercises/exercise_4.cgi b/exercises/vc_exercise_4.cgi → version-control/svn/exercises/exercise_4.cgi
diff --git a/exercises/vc_planets.txt → version-control/svn/exercises/planets.txt b/exercises/vc_planets.txt → version-control/svn/exercises/planets.txt
diff --git a/exercises/vc.markdown → version-control/svn/exercises/svn.markdown b/exercises/vc.markdown → version-control/svn/exercises/svn.markdown
@@ -104,7 +104,7 @@ can check in your changes.
 We have written a special program that modifies the `planets.txt` in your
 repository folder as if it were another user.  Visit the following URL: 
 
-    http://svn.software-carpentry.org/vc_exercise_4.cgi
+    http://svn.software-carpentry.org/exercise_4.cgi
 
 and type in your username.  When you hit submit you should receive a message
 saying `planets.txt` was successfully modified. DO NOT UPDATE YOUR WORKING COPY

diff --git a/exercises/vc_temperature.txt → ...ion-control/svn/exercises/temperature.txt b/exercises/vc_temperature.txt → ...ion-control/svn/exercises/temperature.txt
Original file line number	Diff line number	Diff line change
		@@ -1,5 +1,3 @@


		## Exercise 1

		In the episode on [Randomness](http://software-carpentry.org/4_0/invperc/random)
Expand Down