Packaging and csv export #3
Conversation
|
Add gitignore to the root of the repo: |
pyproject.toml
Outdated
| name = "cloupe_package_nj9" | ||
| version = "0.0.1" | ||
| authors = [ | ||
| { name="Nithin", email="[email protected]" }, |
There was a problem hiding this comment.
{ name="Martin Prete", email="[email protected]" },
{ name="Nithin Mathew Joseph", email="[email protected]" }
There was a problem hiding this comment.
Done. Wait shdn't the email be [email protected] and [email protected]?
There was a problem hiding this comment.
Aliases to full names will also work. But you're right, let's do short usernames only.
| description = "Cloupe Parser" | ||
| readme = "README.md" | ||
| requires-python = ">=3.9.6" | ||
| classifiers = [ |
There was a problem hiding this comment.
Add classifiers:
- Development Status :: 4 - Beta
- Topic :: Scientific/Engineering :: Bio-Informatics
- License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)
There was a problem hiding this comment.
Done. Quick query were these stuff something I needed to know before hand. If so where can I find these info?
There was a problem hiding this comment.
a) You're missing a comma in the list, between "License" and "Programming Language" classifiers.
b) The list of cannonical classifiers are avaiable at https://pypi.org/classifiers/ this is more a legacy thing and not very important as it has fallen out of use, still a nice thing to do properly.
|
|
||
| # Final csv addition | ||
| with open(barcode_clusters, 'w') as barcode_clusters_file: | ||
| barcode_clusters_file.write("Barcodes,{},{}\n".format(cloupe.celltracks[0]["Name"],cloupe.celltracks[1]["Name"])) |
There was a problem hiding this comment.
This code ONLY works if there are two celltracks.
What if there are none? What if there's only one? What if there are 99?
| barcode_clusters_file.write( | ||
| "\n".join( | ||
| [ | ||
| re.sub(r"[()' ]", "", str(pair)) # Remove parentheses, single quotes, and spaces |
There was a problem hiding this comment.
This is also fixed to only support 2 celltracks.
Should be dynamic based on the number of items in cloupe.celltracks.
re.sub(r"[()' ]", "", str(pair)) is very odd
|
|
||
| collection = [] | ||
| # writing the barcodes to the csv files | ||
| with open(barcodes, 'w') as barcodes_file: |
There was a problem hiding this comment.
Could each one of the writes (barcodes, features, and annotations) be an individual function. If so, should they be inside Cloupe class?
Have a look at https://docs.python.org/3.9/library/csv.html for writing CSVs with quoting and all that fun.
There was a problem hiding this comment.
I had been trying various combination of csv writter with the data that we have. I was finding it difficult to dump out the csv properly even when i was using the quoting and quotechar features along with the delimiter. I was thinking if i cud stick without using csv module. Let me know ur thoughts.
Regarding moving the writes as methods. My query would be do i remove the main function entirely and the cloupe.py will remain a class?
|
Related to #2 |
…he root directory
I have formatted the tool to take in input file via the argparse module and at the same time generate output csv files containing Barcodes, Features and Annotations. The build was meant to be used like a n executable hence was made in this format. To execute the code : --> Python3 ./cloupe.py <input_file path>
Once the script is executed it will generate .csv files in the current working directory.