The script currently assumes that the genomes are the same for each dataset.
This was fine until now because the datasets added thus far were from tomato.
The script needs to be further edited to accommodate the fact that this dataset is not tomato.

Updating makeAnnotsXml.py:

Branch: https://bitbucket.org/mdavis4290/molly-genome-browser-visualization/branch/IGBF-3329

Pull Request: https://bitbucket.org/hotpollen/genome-browser-visualization/pull-requests/1/igbf-3329-create-and-test-srp371294-sample

Merged. Moving back to To-Do for testing with makeAnnotsXml.py

Sample sheet:

Branch: https://bitbucket.org/mdavis4290/molly-splicing-analysis/branch/IGBF-3329
Pull Request: https://bitbucket.org/hotpollen/splicing-analysis/pull-requests/10

Notes: Just adding sample sheet. Recent changes were to URL. Still needs to be tested in makeAnnotsXml.py once it is added to team repo

Sample sheet Draft 2:
SRP371294_sample_sheet.xlsx

• Added new URL for SRA dataset

Used solution error 2:

(panda_env) Mollys-iMac:genome-browser-visualization mollydavis333$ export PYTHONPATH=/Users/mollydavis333/Desktop/igbquickload
(panda_env) Mollys-iMac:genome-browser-visualization mollydavis333$ ./makeAnnotsXml.py
Traceback (most recent call last):
  File "/Users/mollydavis333/Desktop/genome-browser-visualization/./makeAnnotsXml.py", line 16, in <module>
    import requests
ModuleNotFoundError: No module named 'requests'

Solution:

python -m pip install requests

Notes: Clone the repos with all of the sample sheets.

pip install openpyxl

Script Ran successfully!

Next Step: Add new sample sheets to script

Error:

(panda_env) Mollys-iMac:genome-browser-visualization mollydavis333$ ./makeAnnotsXml.py                                                                     
Traceback (most recent call last):                                              
  File "/Users/mollydavis333/Desktop/genome-browser-visualization/./makeAnnotsXml.py", line 12, in <module>
    from Quickload import *
ModuleNotFoundError: No module named 'Quickload'

Solution: PYTHONPATH

Documentation for how to run the script "makeAnnotsXml.py" from https://bitbucket.org/hotpollen/genome-browser-visualization/src/main/

1) Clone the repository to your desktop as usual
2) Install or download additional libraries and code needed to run the script.

Required libraries include:

• pandas library - follow instructions for pandas library (google it)
• custom code from Loraine Lab - https://bitbucket.org/lorainelab/igbquickload/src/master/ - follow instructions in the "README" Note that to ensure that the makeAnnots script needs some code modules (not scripts) defined in the Loraine Lab codebase. To ensure that the makeAnnots script can load this, you need to create an environment variable that specifies its location. Use "google" and see instructions in the Loraine Lab code README.

4) Test that when you run the script, it can find the required libraries and custom code from previous step.

To run it it in Terminal, change into the directory containing the script and enter its name. For example:

local aloraine$ cd src/genome-browser-visualization/
local aloraine$ ./makeAnnotsXml.py
local aloraine$ 

Note that if the script runs and does not print any errors, that means it did its job properly.

If there are errors, they will likely have to do with the script not being able to locate either the required pandas library, the required Loraine Lab custom code, or the required data files.

Read the script and compare what you find to the errors message to figure out the problem. This process will take some time as you get more familiar with python, the language of the script, and so on.

Check that the URL column exactly matches URL columns for other datasets from SRA. I'm pretty sure that the URL values for those do not include the "SRP" value.

Look at how the make_annots_xml.py script uses the values coming from the "URL" column when the study is from SRA.