Shell-Scripting.md

@@ -69,8 +69,10 @@ The previous script example is useful to execute multiple programs with a single
 
 ```bash
 #!/bin/bash
-# This script runs a partition function, followed by the prediction of
-# a maximum expected accuracy secondary structure
+# This script runs a partition function, followed by the prediction of a
+# maximum expected accuracy secondary structure.  In this script, the
+# input and output files are given as arguments instead of being defined
+# in the script itself.
 
 # Define a path to a sequence file for the input
 seq_file=$1
@@ -89,5 +91,132 @@ rm foo.pfs
 ```
 Now, the input sequence file and output structure file can be specified when you execute the script.
 
+## String Manipulations
+One common operation is to manipulate strings.  Strings can be combined into a new string and substrings can extracted from a larger string.  One common context for these operations are manipulating file paths.  Two useful commands when dealing with paths is `dirname` and `basename`.  The command `basename` returns the filename from a path by stripping way the directory names.  For example:
+
+```
+[user@host ~]$ basename /home/user/foo.txt
+foo.txt
+```
+
+Similarly, `dirname` returns the directory name information from a given path.  For example:
+```
+[user@host ~]$ dirname /home/user/foo.txt
+/home/user
+```
+Substrings can be extracted using `${string_var:start:length}` construct.  For example:
+```
+[user@host ~]$ foo="HELLO WORLD"
+[user@host ~]$ echo ${foo:0:5}
+HELLO
+```
+Note that the start index begins with 0.  This operation is useful for removing a file extension from a filename to extract a sequence name.  For example:
+
+```
+[user@host ~]$ filename=/home/user/sequence.seq
+[user@host ~]$ dir_name=`dirname $filename`
+[user@host ~]$ echo ${filename:${#dir_name}+1:${#filename}-${#dir_name}-5}
+sequence
+```
+
+A more concise way of performing the same string manipulations would be to use pattern matching using the `%` and `#` operators.  Using the construct `${string_var%pattern}` trims the shortest pattern match from the end of the string.  For example:
+```
+[user@host ~]$ filename=home/user/sequence.seq
+[user@host ~]$ echo ${filename%/*}
+home/user
+```
+
+The construct `${string_var%%pattern}` trims the longest pattern match from the end of the string.  For example:
+```
+[user@host ~]$ filename=home/user/sequence.seq
+[user@host ~]$ echo ${filename%&/*}
+home
+```
+
+The `#` and `##` perform similar functions, except they trim from the front of the string.  For example:
+```
+[user@host ~]$ filename=home/user/sequence.tar.gz
+[user@host ~]$ echo ${filename#*.}
+tar.gz
+[user@host ~]$ echo ${filename##*.}
+gz
+[user@host ~]$ base_name=${filename##*/}
+[user@host ~]$ echo ${base_name%.*}
+sequence.tar
+[user@host ~]$ echo ${base_name%%.*}
+sequence
+```
+
 ## Program Flow
 
+Often, it is useful to be able to alter execution of a script depending on variable values.
+
+### if...else
+
+One of the most basic methods to control the flow a script (or any other program) is by using conditional statements.  
+```bash
+if [ condition ]; then
+   commands when condition is true
+fi
+```
+
+```bash
+if [ condition ]; then
+   commands when condition is true
+else
+   commands when condition is false
+fi
+```
+
+#### Comparisons
+ Bash Comparison | Math Equivalent
+:----:|:----:
+-lt|	 < 
+-gt|	>
+-le|	<=
+-ge|	>=
+-eq|	==
+-ne|	!=
+
+## Loops
+### For loops
+For loops will execute a section of the script a set number of multiple times.
+
+The general syntax for a For loop in bash is:
+```bash
+#!/bin/bash
+for i in 1 2 3 4 5
+do
+   echo "Hello $i"
+done
+```
+
+The output of this is:
+```
+Hello 1
+Hello 2
+Hello 3
+Hello 4
+Hello 5
+```
+
+An equivalent loop is:
+```bash
+#!/bin/bash
+for i in {1..5}
+do
+   echo "Hello $i"
+done
+```
+
+You can also use a for loop to run a set of commands for all files in a folder
+```bash
+ #!/bin/bash
+
+input_dir=/home/user/Input_Files
+
+for filename in $input_dir/*; do
+    echo $filename
+done
+```
+Here, the `*` character represents a wildcard.  If the for statement was instead replaced with `for filename in $input_dir/*.txt; do`, the loop would print the filename of every file whose path began with `/home/user/Input_Files` and ended with `.txt`.
\ No newline at end of file