From 468381ccaf552fb71460e2569926a7d442d7ad17 Mon Sep 17 00:00:00 2001
From: tobyhodges <tbyhdgs@gmail.com>
Date: Tue, 8 Dec 2015 13:26:34 +0100
Subject: [PATCH] added a few more biology-specific examples
---
linux_intermediate/basic_scripting.rst | 86 ++++++++++++++++----------
1 file changed, 53 insertions(+), 33 deletions(-)
diff --git a/linux_intermediate/basic_scripting.rst b/linux_intermediate/basic_scripting.rst
index db1f4f6..924c6a1 100644
--- a/linux_intermediate/basic_scripting.rst
+++ b/linux_intermediate/basic_scripting.rst
@@ -179,29 +179,35 @@ or based on the success of the respective previous command:
Example: Create a directory and, if not successful, print an error message::
- $ mkdir /bin/a || echo "Could not create directory a"
+ $ mkdir /bin/a || echo "mkdir didn't work!"
mkdir: cannot create directory `/bin/a': Permission denied
- Could not create directory a
+ mkdir didn't work!
$
- Example: Warn if a directory doesn't exist: ::
+ Example: Decompress a gzipped file if it exists, or download it if not: ::
- $ cd /etc || echo "/etc is missing!"
- $ cd /nowhere >&/dev/null || echo "/nowhere does not exist"
- /nowhere does not exist
+ $ gzip -d 2W73.pdb || wget "http://www.rcsb.org/pdb/files/2W73.pdb.gz"
$
+You can mix multiple ``&&`` and ``||`` controls into a single line.
+
Example: Create a directory and, if successful, change into it, if not successful, print an error message::
$ mkdir /bin/a && cd a || echo "Could not create directory a"
mkdir: cannot create directory `/bin/a': Permission denied
Could not create directory a
$
- $ mkdir ~/bin/a && cd a || echo "Could not create directory a"
+ $ mkdir ~/a && cd ~/a || echo "Could not create directory a"
$ pwd
/home/fthommen/a
$
+ Example: Count the heterogens described in a gzipped PDB file or, if it doesn't exist,
+ download the file::
+
+ $ gzip -c 4ZZN.pdb.gz && sed -n '/^HET /p' || wget "http://www.rcsb.org/pdb/files/4ZZN.pdb.gz"
+ $
+
*( cmds )* --
Group commands to create one single output stream: The commands are run in a subshell (i.e. a new shell is opened to run them):
@@ -210,7 +216,7 @@ or based on the success of the respective previous command:
$ pwd
/home/fthommen
$ (cd /etc; ls)
- [... directory listing here ...]
+ [... etc directory listing here ...]
$ pwd
/home/fthommen
$
@@ -362,20 +368,20 @@ B) Evaluating of conditions or comparisons:
Examples: Test for the existence of /etc/passwd::
- if [ -e /etc/passwd ]
+ if [ -e ./sequence_files ]
then
- echo /etc/passwd exists
+ ls -1 ./sequence_files/*.fasta
else
- echo /etc/passwd does NOT exist
+ echo no sequence_files directory here
fi
or::
- if test -e /etc/passwd
+ if test -e ./sequence_files
then
- echo /etc/passwd exists
+ ls -1 ./sequence_files/*.fasta
else
- echo /etc/passwd does NOT exist
+ echo no sequence_files directory here
fi
@@ -403,13 +409,13 @@ The basic syntax :index:`is <breaksw>`:
| case variable in | switch (variable) |
| pattern1) | case pattern1: |
| commands | commands |
-| ;; | breasksw |
+| ;; | breaksw |
| pattern2) | case pattern2: |
-| commands | commands |
-| ;; | breaksw |
+| commands | commands |
+| ;; | breaksw |
| *) | default: |
-| commands | commands |
-| ;; | endsw |
+| commands | commands |
+| ;; | endsw |
| esac | |
+---------------------------------------+---------------------------------------+
@@ -426,14 +432,27 @@ Example:
Check if /opt/ or /usr/ paths are contained in ``$PATH``: ::
case $PATH in
- */opt/* | */usr/* )
- echo /opt/ or /usr/ paths found in \$PATH
+ */opt/* )
+ echo /opt/ paths found in \$PATH
+ ;;
+ */etc/* )
+ echo /etc/ paths found in \$PATH
;;
*)
echo '/opt and /usr are not contained in $PATH'
;;
esac
+ or
+
+ case $PATH in
+ */opt/* | */etc/* )
+ echo /opt/ or /etc/ paths found in \$PATH
+ ;;
+ *)
+ echo '/opt and /usr are not contained in $PATH'
+ ;;
+ esac
Loops
-----
@@ -460,16 +479,18 @@ list of given values and run the given statements for reach run:
*list* is a list of strings, separated by whitespaces
Examples:
- List all files in /tmp in a bulleted list: ::
+ List filenames and count number of sequences in every FASTA file in ./sequence_files: ::
- for FILE in /tmp/*
+ for FILE in ./sequence_files/*.fasta
do
echo " * $FILE"
+ grep -c '\>' $FILE
done
or
- for FILE in `ls /tmp`
+ for FILE in `ls ./sequence_files/*.fasta`
do
echo " * $FILE"
+ grep -c '\>' $FILE
done
@@ -541,10 +562,6 @@ options and arguments.
Configurable Scripts
--------------------
-Any value - be it paths, commands or options - that is specific to individual
-applications or your script, should not be "hardcoded" (i.e. used literally
-within the script) but assigned to variables:
-
Using Variables
^^^^^^^^^^^^^^^
@@ -553,7 +570,7 @@ applications or your script, should not be hardcoded (i.e. used literally
within the script). Instead you should use variables to refer to them:
Bad example:
- You have to change two instances of the path each time you want to list an other directory::
+ You have to change two instances of the path each time you want to list another directory::
#!/bin/sh
@@ -561,7 +578,7 @@ Bad example:
ls /etc
Good example:
- The path is now in a variable and only one instance has to be changed each time (less work, less errors)::
+ The path is now in a variable and only one instance has to be changed each time (less work, fewer errors)::
#!/bin/sh
@@ -570,7 +587,7 @@ Good example:
echo "The directory $MYDIR contains the following files:"
ls $MYDIR
-Of course, you'll still have to modify the script each time you want to list the content of an other directory. A more flexible way of customization would be to use a settings file.
+Of course, you'll still have to modify the script each time you want to list the content of another directory. A more flexible way of customization would be to use a settings file.
Using a Settings File
^^^^^^^^^^^^^^^^^^^^^
@@ -599,7 +616,7 @@ Defining your own Commandline Options and Arguments
---------------------------------------------------
The best way to configure a script is to allow for your own commandline options
-and arguments. Commandline arguments are available the script as so-called
+and arguments. Commandline arguments are available within the script as so-called
:index:`positional parameters` ``$1``, ``$2``, ``$3``: etc. ``$0``: contains the name of the script. The
variables important when dealing with commandline parameters are:
@@ -743,7 +760,7 @@ Filenames and Paths
-------------------
If possible, try to avoid any special characters (blanks, semicolons (";"),
-colons (":"), backslashes ("\") etc.) in file and directory names. All these
+colons (":"), backslashes ("\\") etc.) in file and directory names. All these
special characters can lead to problems in scripted processing. Instead, stick
to alphanumeric characters (a-z, 0-9), dots ("."), dashes ("-") and underscores
("_"). Additionally sticking to lowercase characters helps avoiding mistypes
@@ -814,6 +831,9 @@ file in /tmp and print its name: ::
/tmp/tmp.Yaafh19370
$
+You can take advantage of the fact that mktemp returns the name of the created file,
+to capture this file name and use it in your script.
+
Cleaning up Temporary Files
---------------------------
--
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