# Example 1: Word Count (wc) In this example, you will: * Learn to write a native DNAnexus applet that executes a Python program * Use the `dxpy` module to download and upload files * Use the Python `subprocess` module to execute an external process and check the return value ## Getting Started We'll use the same *scarlet.txt* file from the `bash` version of the `wc` applet. Start off using `dx-app-wizard` and define the same inputs and outputs as before, but be sure to choose *Python* for the *Programming language*: ``` Template Options You can write your app in any programming language, but we provide templates for the following supported languages: Python, bash Programming language: Python ``` ## Python Template The Python template looks like the following: {% code title="python\_wc.py" overflow="wrap" lineNumbers="true" %} ```python #!/usr/bin/env python # python_wc 0.1.0 # Generated by dx-app-wizard. # # Basic execution pattern: Your app will run on a single machine from # beginning to end. # # See https://documentation.dnanexus.com/developer for documentation and # tutorials on how to modify this file. # # DNAnexus Python Bindings (dxpy) documentation: # http://autodoc.dnanexus.com/bindings/python/current/ import os import dxpy @dxpy.entry_point('main') # 1 def main(input_file): # 2 # The following line(s) initialize your data object inputs on the platform # into dxpy.DXDataObject instances that you can start using immediately. input_file = dxpy.DXFile(input_file) # 3 # The following line(s) download your file inputs to the local file system # using variable names for the filenames. dxpy.download_dxfile(input_file.get_id(), "input_file") # 4 # Fill in your application code here. # The following line(s) use the Python bindings to upload your file outputs # after you have created them on the local file system. It assumes that you # have used the output field name for the filename for each output, but you # can change that behavior to suit your needs. outfile = dxpy.upload_local_file("outfile") # 5 # The following line fills in some basic dummy output and assumes # that you have created variables to represent your output with # the same name as your output fields. output = {} output["outfile"] = dxpy.dxlink(outfile) # 6 return output # 7 dxpy.run() ``` {% endcode %} 1. [entry\_point](http://autodoc.dnanexus.com/bindings/python/current/dxpy_utils.html#dxpy.utils.exec_utils.entry_point): DNAnexus execution environment entry point 2. The `input_file` listed in the `inputSpec` is passed to `main`. 3. Create a [DXFile](http://autodoc.dnanexus.com/bindings/python/current/dxpy_dxfile.html#dxpy.bindings.dxfile.DXFile) object. 4. Download the input file. 5. Upload the local output file. 6. Add the DX file ID to the `output` dictionary. 7. Return the `output` Update *src/python\_wc.py* to the following: {% code title="python\_wc.py" overflow="wrap" lineNumbers="true" %} ```python #!/usr/bin/env python import dxpy import sys from subprocess import getstatusoutput # 1 @dxpy.entry_point("main") def main(input_file): local_file = "input_file.txt" # 2 output_file = "output.txt" # 3 input_file = dxpy.DXFile(input_file) # 4 dxpy.download_dxfile(input_file.get_id(), local_file) # 5 rv, out = getstatusoutput(f"wc {local_file} > {output_file}") # 6 if rv != 0: # 7 sys.exit(out) outfile = dxpy.upload_local_file(output_file) # 8 return {"outfile": dxpy.dxlink(outfile)} # 9 dxpy.run() ``` {% endcode %} 1. Import the [`subprocess.getstatusoutput`](https://docs.python.org/3/library/subprocess.html#subprocess.getstatusoutput) function. 2. Use the local filename *input\_file.txt*. 3. The output file will be called *output.txt*. 4. *Shadow* the `input_file` variable, overwriting it with the creation of a new [`DXFile`](http://autodoc.dnanexus.com/bindings/python/current/dxpy_dxfile.html#dxpy.bindings.dxfile.DXFile) object. 5. Call [`dxpy.download_dxfile`](http://autodoc.dnanexus.com/bindings/python/current/dxpy_dxfile.html#dxpy.bindings.dxfile_functions.download_dxfile) to download the input file identified by the file ID to the `local_file` name. 6. Execute `wc` on the local input file and redirect (`>`) the output to the chosen output filename. This function returns a tuple containing the process's return value and output (STDOUT/STDERR). 7. If the return value is not zero, use [`sys.exit`](https://docs.python.org/3/library/sys.html#sys.exit) to abort the program with the output from the system call. 8. If the program makes it to this point, the output file should have been created to upload. 9. Return a Python dictionary with the DNAnexus link to the new `outfile` object. NOTE: Portable Operating System Interface (POSIX) standards dictate that processes return `0` on success (i.e., zero errors) and some positive integer value (usually in the range 1-127) to indicate an error condition. Run `dx build` to build the applet. Create an *job\_input.json* file with the file ID of your input: ``` { "input_file": { "$dnanexus_link": "file-GgGX7Y8071x46B02JGb515pB" } } ``` Run your applet with the input file using `--watch` to see the output: ``` $ dx run applet-GgGX740071xJY20Gjkp0JYXB -f python_wc/job_input.json \ -y --watch \ --destination project-GXY0PK0071xJpG156BFyXpJF:/output/python_wc/ Using input JSON: { "input_file": { "$dnanexus_link": "file-GgGX7Y8071x46B02JGb515pB" } } Calling applet-GgGX740071xJY20Gjkp0JYXB with output destination project-GXY0PK0071xJpG156BFyXpJF:/output/python_wc Job ID: job-GgGX8P0071x1yfFPkJ8662gQ Job Log ------- Watching job job-GgGX8P0071x1yfFPkJ8662gQ. Press Ctrl+C to stop watching. * Python implementation of wc (python_wc:main) (running) job-GgGX8P0071x1yfFPkJ8662gQ kyclark 2024-02-23 16:03:24 (running for 0:01:39) 2024-02-23 16:11:36 Python implementation of wc INFO Logging initialized (priority) 2024-02-23 16:11:36 Python implementation of wc INFO Logging initialized (bulk) 2024-02-23 16:11:40 Python implementation of wc INFO Setting SSH public key 2024-02-23 16:11:42 Python implementation of wc STDOUT dxpy/0.369.0 (Linux-5.15.0-1053-aws-x86_64-with-glibc2.29) Python/3.8.10 2024-02-23 16:11:43 Python implementation of wc STDOUT Invoking main with {'input_file': {'$dnanexus_link': 'file-GgGX7Y8071x46B02JGb515pB'}} * Python implementation of wc (python_wc:main) (done) job-GgGX8P0071x1yfFPkJ8662gQ kyclark 2024-02-23 16:03:24 (runtime 0:01:36) Output: outfile = file-GgGXGFj0FbZxjvk1jZPJPkG2 ``` I can inspect the contents of the output file: ``` $ dx cat file-GgGXGFj0FbZxjvk1jZPJPkG2 8596 86049 513778 input_file.txt ``` I can verify this is correct by piping the input file to a local execution of `wc`: ``` $ dx cat file-GgGX7Y8071x46B02JGb515pB | wc 8596 86049 513778 ``` ## Debugging Locally You can shorten the `build`/`run` development cycle by naming the JSON input *job\_input.json* and executing the Python program locally: ``` $ python3 src/python_wc.py Invoking main with {'input_file': {'$dnanexus_link': 'file-GgGX7Y8071x46B02JGb515pB'}} ``` This will download the input as *input\_file.txt* and then create a new local file with the system call: ``` $ cat output.txt 8596 86049 513778 input_file.txt ``` ## Review * You have now translated the `bash` applet for running `wc` into a native DNAnexus Python applet. * You were introduced to the `dxpy` module that provides functions for making API calls. * You used `subprocess.getstatusoutput` to call an external process and interpret the return value for success or failure. 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