EnsemblX

Current Version: v2.0.1 (Fixed bug related to xlrd engine used to read *.xlsx files by reverting from Python 3.9 to 3.8 and recompiling the EnsemblX executable.)

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Description

EnsemblX is a niche, but potentially useful, Python applet that seeks to speed up and simplify the retrieval of short gene descriptions (and other relevant data) for barley genes using their Gene Stable IDs to reference the matching annotations from Ensembl Plants and BARLEX. EnsemblX is a free-time endeavor used mainly as a hands-on project to encapsulate my experimentation with applying programming to biological data handling as I learn Python.

Getting Started

To learn how to download and use EnsemblX visit the wiki here on GitHub.

Origin

In its first form, EnsemblX was an R script (here tagged as v1.0.0-pre2.0.0) that used web scraping to pull down the annotation information from each genome browser's web interface; however, as EnsemblX progressed (and as I progressed in my programming knowledge) it became apparent that web scraping was slow and discouraged on the specific pages the R script scraped. Therefore an alternative data retrieval method was necessary.

Version 2

In the Python-based EnsemblX Version 2, the Ensembl Plants data is now retrieved using the Ensembl REST API POST lookup/id functionality and the BARLEX data is referenced from a local, pre-processed copy of the data retrieved as the 160517_Hv_IBSC_PGSB_r1_CDS_HighConf_REPR_annotation.fasta.gz dataset (available here). The code for pre-processing this data can be found in the data_pre_processing.py Python script.

EnsemblX was created to facilitate the typically repetitive, manual process of copying and pasting the relevant information for select genes of interest through each genome browser's web interface. As such, EnsemblX Version 2 tries to simplify the process even further by providing a basic user interface to interact with the underlying workflow. This user interface is currently built using tkinter with ttk widgets and the workflow relies on pandas to manage and manipulate the incoming and outgoing data.

Below are screenshots of the two main GUI pages implemented in EnsemblX Version 2. The start page is the opening page of the applet that links to the other GUI pages (the Excel page and a disabled button for a future quick reference page). The start page also provides easy reference within the GUI to the GitHub wiki and repository.

Start Page	Excel Page
(Screenshots taken from EnsemblX v2.0.0)

Notes on Bugs and Features for Future Versions

• The process for creating the executable version of EnsemblX with pyinstaller currently only works for creating the Windows executable. Trial and error has not yet led to a functioning macOS application.
• While the underlying workflow is running, the GUI often becomes unresponsive until the process is complete. The solution may involve running the underlying workflow in a separate processing thread so that the tkinter mainloop() is always free to update the GUI widgets.
• There is no option for selecting which data fields to return from each source in the final output so the final Excel file contains all the information returned from the selected source(s). Implementing a hierarchical list of the data fields available from each source (with checkboxes to select them) could be used to generate a string of the desired data fields by which to filter the final pandas DataFrame before writing to Excel.
• The "File Selected" text on the Excel page retains the originally selected file if the open file window is re-opened and closed without selecting a new file. Should revert to "None".
• Change mentions of "Excel" on the GUI to the more generalized "Spreadsheet" because EnsemblX can also read and write *.ods files from OpenOffice.
• The first implementation of the quick reference feature (currently removed except for a disabled placeholder button on the start page of the GUI) could not be formatted properly using my current understanding of tkinter and the ttk widgets. Perhaps creating and destroying frames and widgets as needed with the destroy() method (as opposed to stacking and raising them with the show_frame() method) would better support displaying the varying format of the quick reference output on-screen.