AWK: convert into lower or upper cases

In order to convert a bash variable to lower case with awk, just use this command:

If you want to convert the content of a file (called data.csv) to lower case:

Of course to convert into upper case, simply use the function toupper() instead of tolower().

Note also that a better tool to avoid issues with special characters might be the tr unix command:

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How to sort a dictionary by values in Python

By definition, dictionary are not sorted (to speed up access). Let us consider the following dictionary, which stores the age of several persons:

If you want to sort this dictionary by values (i.e., the age), you must be another data structure such as a list, or an ordered dictionary.

Use the sorted function and operator module

Sorted_d is a list of tuples sorted by the second element in each tuple. Each tuple contains the key and value for each item found in the dictionary. If you look at the content of this variable, you should get:

Use the sorted function and lambda function

If you do not want to use the operator module, you can use a lambda function:

The computation time is of the same order of magnitude as with the operator module. Would be interesting to test on large dictionaries.

Use the sorted function and return an ordered dictionary

In the previous methods, the returned objects are list of tuples. So we do not have a dictionary anymore. You can use an OrderedDict if you prefer:

Use sorted function and list comprehension

another method consists in using list comprehension and use the sorted function on the tuples made of (value, key).

Here the output is a list of tuples where each tuple contains the value and then the key:

Python 3.6 native sorting

In Python 3.6, the iteration through a dictionary is sorted. Consequently, you can just use:

The other advantage with this method is speed and the ability to return tuples as pairs of key/value or value/key.


Here is a quick benchmark made using the small dictionary from the above examples. Would be interesting to redo the test with a large dictionary. This was done within a PYthon 3.6 environment.

What you can see is that the native Python dictionary sorting is pretty cool followed by the combination of the lambda + list comprehension method. Overall using one of these four methods would be equivalent though (factor 2/3 at most).

This image was created with the following code.

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Python: how to copy a list

To explain how to create a copy of a list, let us first create a list. We will use a simple list of 4 items:

Why do we want to create a copy anyway ? Well, because in Python, this assignement creates a reference (not a new independent variable):

To convince yourself, change the first item of list2 and then check the content of list1, you should see that the two lists have been modified and contain the same items.

So, to actually copy a list, you have several possibilities. From the simplest to the most complex:

  • you can slice the list.
  • you can use the list() built in function
  • you can use the copy() function from the copy module. This is slower than the previous methods though.
  • finally, if items of the list are objects themselves, you should use a deep copy (see example below):
  • To convince yourself about the interest of the latter method, consider this list:

    you should see that changing list2, you also changed list1. If this is not the intended behviour, you should consider using the deepcopy.

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    Python: ternary operator

    In C language (and many other languages), there is a compact ternary conditional operator that is a compact if-else conditional construct. For instance, in C, a traditional if-else construct looks like:

    and the equivalent ternary operator looks like:

    As in the if-else code, only one expression x or y is evaluated.

    In Python, from version 2.5, you would write:

    More formally the ternary operator is written as:

    So condition is evaluated first then either x or y is returned based on the boolean value of condition.

    You can use ternary operator within list comprehension. For example:

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    Difference between __repr__ and __str__ in Python

    When implementing a class in Python, you usually implement the __repr__ and __str__ methods.

    1. __str__ should print a readable message
    2. __repr__ should print a message that is unambigous (e.g. name of an identifier, class name, etc).

    You can see __str__ as a method for users and __repr__ as a method for developers.

    Here is an implementation example for a class that simply stores an attribute (data).

    __str__ is called when a user calls the print() function while __repr__ is called when a user just type the name of the instance:

    By default when no __str__ or __repr__ methods are defined, the __repr__ returns the name of the class (Length) and __str__ calls __repr__.

    Now, let us define the __repr__ method ourself to be more explicit:

    we could use it as follows:

    When using the print() function in Python, the __str__ is called (if found) and otherwise, __repr__.

    so now __repr__ and __str__ have different behaviours:

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    python: how to merge two dictionaries

    Let us suppose two dictionaries storing ages of different individuals:

    If you do mind losing the contents of either list1 or list2 variable, you can update one of the other as follows:

    Now list1 variable contains:

    while list2 is unchanged.

    Usually, this is not what you want though. Instead, you would prefer to create a third variable keeping list1 and list2 unchanged.

    In Python 3.5 or greater, you can use the following syntax:

    In Python 2 or 3.4 and below, you need to copy one of the variable and update it:

    The second method is more generic and would be more backward compatible (if you plan to provide your code to Python 2 users. Indeed, it would work for Python 2 and 3. However, it would be slower for Python 3.5 users (and above).

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    Search for a pattern in a set of files using find and grep commands

    A common task for developers is to search for a pattern amongst a bunch of files that are in different directories.

    For instance, you are looking for the pattern “import sys” within a set of Python files. Those files are in sub directories mixed with other documents.

    You can use the find command (to look for files ending with the py extension) and redirect those files to the grep command to search for the pattern “import sys” within all files found by the find command:

    find . -name "*py" | xargs grep "import sys"

    Note the double quotes and the use of the xargs command to scan the content of the files (not their names).

    Of course, you can use all kind of wildcards:

    find . -name "*py" | xargs grep "import sys"

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    okular: export annotations in the PDF file

    One open source software to add annotations under Linux is okular (

    One can add annotations easily (go to Tools, tick review, or just type F6).

    Then, it is time to save your document or to send it to a collaborator but wait a minute: we do not see the annotations when using acroread reader !! No worries, plenty of resources tell you to go to File/save as

    Seems to work indeed. You quit, open the file and there you can see the annotations. Now, I use xpdf to read the PDF file. And here nothing. Oh, and I send the PDF to a journal review; they include the PDF inside another one and there no annotations either….

    Final solution: instead of File/Save as, just print the document in … a PDF file: File/Print

    This worked for me.

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    No more space left on /tmp under Fedora

    Under Fedora, one of my software requires more than 4Gb of temporary space and I realised that the /tmp directory is limited to 4Gb. In order to increase the /tmp directory, just edit the /etc/fstab file and add this line (to extend to 8Gb instead of 4Gb):

    Then, as root:

    That’s it. You can check that you have now 8Gb available in /tmp by typing

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    blasr (pacbio) installation on fedora box

    I wanted to use blasr tool for Pacbio mapping and had difficulties in using or installing the tool. I first use a local installation of the tool on the provided cluster and it look like the installation was quite old. I then use a bioconda version. The latest version (5.3) was not working on my system (missing library) and this was reported. The previous version worked (5.2) but was missing a needed configuration flag. So, I decided to follow the instructions from pacbio to install a local version. That was not straightforward but finally got it to work. My platform is Fedora 23 and the instructions were given for ubuntu or centos 6.

    First, download the source code:

    This command installs zlib, bzip2, boost and hdf5 to start with.
    The first issue arised from an error in the compilation of the hdf5 dependency due to missing iostream in the compilation of the hdf5 library

    The solution was to edit the Makefile in workspace/hdf5-1.8.16/c++
    and to comment this line (adding a # character in front))

    Come back to the main pitchfork directory, type the make command again (see above). Another failure due to similar compilation error related to the namespace occured. Again, I edited the Makefile in
    workspace/hdf5-1.8.16/c++/test/Makefile and commented the same line.

    Next, I got a linking issue

    This was solved by installing the stdc++ static library. I figure out the solution by typing:

    to see that none of the standard path could find the library despite the presence of the /usr/lib/

    Again, type

    I got

    so again, needed to find the culprit: a Makefile and it was in
    In workspace/hdf5-1.8.16/c++/hl/test/Makefile . Again comment the same line as shown above.

    Back to blasr, the make then failed when trying to install ncurses.

    Here I tried a different strategy and tried to use the packages installed with my conda environement. To do so, I edited the and added:

    Then, same issue with samtools, so added

    Then, there was an error in the ./bin/pitchfork module due to a Python 3 issue (I had already switch all print “” to print(“”). Here, the issue was

    Just replace _out[0] with str(_out[0])

    Then, blasr compiles successfully…time to run it; The executable seems to be in workspace/blasr/blasr:

    ./workspace/blasr/blasr: error while loading shared libraries: cannot open shared object file: No such file or directory

    Here, you need to add a bunch of path to your LD_LIBRARY_PATH:

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