Snakefiles are Python code

Overview

Teaching: 30 min
Exercises: 30 min

Questions

• How can I automatically manage dependencies and outputs?

• How can I use Python code to add features to my pipeline?

Objectives

• Use Python variables, functions, and imports in a Snakefile.

• Learn to use the run action to execute Python code as an action.

Despite our efforts, our pipeline still has repeated content, for instance the names of input and output files (dependencies and targets). Our zipf_test rule, for instance, is extremely clunky. What happens if we want to analyze books/sierra.txt as well? We’d have to update everything!

rule zipf_test:
    input:  'zipf_test.py', 'abyss.dat', 'last.dat', 'isles.dat'
    output: 'results.txt'
    shell:  'python {input[0]} {input[1]} {input[2]} {input[3]} > {output}'

Let’s try to improve this rule. One thing you’ve probably noticed is that all of our rules are using Python strings. Other data structures work too - let’s try a list:

rule zipf_test:
    input:
        cmd='zipf_test.py',
        dats=['abyss.dat', 'last.dat', 'isles.dat']
    output: 'results.txt'
    shell: 'python {input.cmd} {input.dats} > {output}'

After updating your rule, run snakemake clean and snakemake -p to confirm that the pipeline still works.

Named Dependencies

Note that we also had to switch to using named dependencies. This was required since the first input, zipf_text.py, should not be in the list of input files.

Inputs: named vs indexed?

Having seen the use of both named and indexed dependencies, which approach do you prefer?

Which approach do you think leads to Snakefiles that are easier to read and maintain?

The use of a list for the input files illustrates a key feature of Snakemake: Snakefiles are just Python code.

We can make our list into a variable to demonstrate this. Let’s create the global variable DATS and use it in our zipf_test and dats rules:

DATS=['abyss.dat', 'last.dat', 'isles.dat']

# generate summary table
rule zipf_test:
    input:
        cmd='zipf_test.py',
        dats=DATS
    output: 'results.txt'
    shell: 'python {input.cmd} {input.dats} > {output}'

rule dats:
    input: DATS

Great! One more step towards reducing code duplication. Now there is just one place to update the list of files to process.

Update your Snakefile

Update your Snakefile with the DATS global variable.

Try recreating both the dats and results.txt targets (run snakemake clean in between).

Solution

See .solutions/snakefiles_are_python/Snakefile_dats_list for a full Snakefile. Otherwise, just refer to the code extracts above and modify your own file.

When are Snakefiles executed?

The last example illustrated that we can use arbitrary Python code in our Snakefile. It’s important to understand when this code gets executed. Let’s add a print statement to the top of our Snakefile:

print('Snakefile is being executed!')

DATS=['abyss.dat', 'last.dat', 'isles.dat']

# generate summary table
rule zipf_test:
    input:
# more output below

Now let’s clean up our workspace with snakemake clean:

snakemake clean

Snakefile is being executed!
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	clean
	1

rule clean:
    jobid: 0

Finished job 0.
1 of 1 steps (100%) done

Now let’s re-run the pipeline…

snakemake

Snakefile is being executed!
Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	3	count_words
	1	zipf_test
	4

rule count_words:
    input: wordcount.py, books/last.txt
    output: last.dat
    jobid: 3
    wildcards: file=last

Finished job 3.
1 of 4 steps (25%) done

rule count_words:
    input: wordcount.py, books/abyss.txt
    output: abyss.dat
    jobid: 1
    wildcards: file=abyss

Finished job 1.
2 of 4 steps (50%) done

rule count_words:
    input: wordcount.py, books/isles.txt
    output: isles.dat
    jobid: 2
    wildcards: file=isles

Finished job 2.
3 of 4 steps (75%) done

rule zipf_test:
    input: zipf_test.py, abyss.dat, last.dat, isles.dat
    output: results.txt
    jobid: 0

Finished job 0.
4 of 4 steps (100%) done

Let’s do a dry-run:

snakemake -n

Snakefile is being executed!
Nothing to be done.

In every case, the print() statement ran before any of the actual pipeline code. What we can take away from this is that Snakemake executes the entire Snakefile every time we run snakemake, even for a dry-run. Because of this we need to be careful and only put tasks that do “real work” (changing files on disk) inside rules.

Common tasks, such as building lists of input files that will be reused in multiple rules are a good fit for Python code that lives outside the rules.

Is your print output appearing last?

On some systems, output is buffered. This means that nothing is actually output until the buffer is full. While this is more efficient, it can delay the output from the print command.

In my testing on Windows using the combination of Git Bash and Anaconda, the print statement is buffered, resulting in the text printing to the terminal after all the Snakemake output. If this is happening to you, tell the print statement to force a flush of the output buffer:

print("Snakefile is being executed!", flush=True)

You should then see the printed text before the Snakemake output, confirming that this code executes first.

Using functions in Snakefiles

In our example here, we only have 4 books (and just 3 are being processed). But what if we had 700 books to be processed? It would be a massive effort to update our DATS variable to add the name of every single book’s corresponding .dat filename.

Fortunately, Snakemake ships with several functions that make working with large numbers of files much easier. The two most helpful ones are glob_wildcards() and expand(). Let’s start a Python session to see how they work.

This can be done in any Python environment

You can use any Python environment for the following code exploring expand() and glob_wildcards(). The standard Python interpreter, ipython, or a Jupyter Notebook. It’s up to personal preference and what you have installed.

On Windows, calling python from Git Bash does not always work. It is better to use the Anaconda start menu entries to run a Python prompt and then run python from there.

Make sure you change to your Snakefile directory before launching Python.

In this example, we will import these Snakemake functions directly in our Python session.

Importing is not required in a Snakefile

You don’t need to import the Snakemake utility functions within your Snakefile - they are always imported for you.

So in your chosen Python environment, run the following:

from snakemake.io import *

Generating file names with expand()

The first function we’ll use is expand(). expand() is used quite literally, to expand snakemake wildcards into a set of filenames:

expand('folder/{wildcard1}_{wildcard2}.txt', wildcard1=['a', 'b', 'c'], wildcard2=[1, 2, 3])

['folder/a_1.txt',
 'folder/a_2.txt',
 'folder/a_3.txt',
 'folder/b_1.txt',
 'folder/b_2.txt',
 'folder/b_3.txt',
 'folder/c_1.txt',
 'folder/c_2.txt',
 'folder/c_3.txt']

In this case, expand() created every possible combination of filenames from the two wildcards. Nice! Of course, this still leaves us needing to get the values for wildcard1 and wildcard2 in the first place.

Get wildcard values with glob_wildcards()

To get a set of wildcards from a list of files, we can use the glob_wildcards() function. It matches the given pattern against files on the file system, returning a named tuple containing all the matches. Let’s try grabbing all of the book titles in our books folder:

glob_wildcards('books/{example}.txt')

Wildcards(example=['isles', 'last', 'abyss', 'sierra'])

In this case, there is only one wildcard, {example}. We can extract the values for name by getting the example property from the output of glob_wildcards():

glob_wildcards('books/{example}.txt').example

['isles', 'last', 'abyss', 'sierra']

Putting it all together

Using the expand() and glob_wildcards() functions, modify the pipeline so that it automatically detects and analyzes all the files in the books/ folder.

Hint

Use expand() and glob_wildcards() together to create the value of DATS.

Solution

The critical change is to the assignment of DATS, building it dynamically from the input *.txt file names.

DATS = expand('{book}.dat', book=glob_wildcards('./books/{book}.txt').book)

See .solutions/snakefiles_are_python/Snakefile_glob_dats for a full Snakefile using this approach.

Using Python code as actions

One very useful feature of Snakemake is the ability to execute Python code instead of just shell commands. Instead of shell: as an action, we can use run: instead.

Add the following to your snakefile:

# at the top of the file
import glob
import os

# add as the last rule (we don't want it to be the default)
rule print_book_names:
    run:
        print('These are all the book names:')
        for book in glob.glob('books/*.txt'):
            print(book)

Upon execution of the corresponding rule, Snakemake runs our Python code in the run: block:

snakemake --quiet print_book_names

Provided cores: 1
Rules claiming more threads will be scaled down.
Job counts:
	count	jobs
	1	print_book_names
	1

rule print_book_names:
    jobid: 0

These are all the book names:
books/isles.txt
books/last.txt
books/abyss.txt
books/sierra.txt
Finished job 0.
1 of 1 steps (100%) done

Note the --quiet option

--quiet or -q suppresses a lot of the rule progress output from Snakemake. This can be useful when you just want to see your own output.

Key Points

• Snakefiles are Python code.

• The entire Snakefile is executed whenever you run snakemake.

• All actual work should be done by rules.

• A shell action executes a command-line instruction.

• A run action executes Python code.