jcasadogp / bacterial_growth

This repository contains the script developed for my Master Thesis in gut bacterial growth curves.

bacterial_growth

Environment set up

First, you need to set up the environment that contain all the packages that will be used by the program. To do so, run the following commands:

cd envs/
conda env create -f environment.yml

Hello

bacterial_growth's Issues

Plot one technical replicates

Change the style of the line such that we can differentiate between the measured points and the lines that are binding those points. In other plotting options it is not necessary has we have the standard deviation bars.

test data set, example of how to run

Consider adding a test data set and a brief tutorial with the main functions developed. 💯

Combination of user input parameters in --createInfoFile

With the positional argument createInfoFile, the user can introduce 3 optional arguments: --num_studies, --num_biological_replicatesand --num_perturbations. The problem is because of the combinations that can be created with this input parameters.
--num_studies is already limited to 0 or 1; only one study can be added at a time.
Is --num_biological_replicates is 1, -num_perturbations can be 0, 1 or N, as all the perturbations will be added in that single new experiment. But, if -num_biological_replicates is N, the perturbations we may add after that will all be included in the last biological replicate introduced in the database.
Solve this in way that is easy for the user to understand the combinations he can make.

Lab files analysis .sh file

When I tried to populate the DB with the command:

python3 main.py populateDB --info_file ../../Desktop/local_thesis_files/yml_files/study_information.yml

The study_information.yml contained these directories for files:

value: /Users/julia/Desktop/local_thesis_files/BT_mucin_RNAseq_3.txt

I got the following error (which started a cascade or errors):

ls: /Users/julia/Desktop/local_thesis_files/BT_mucin_RNAseq_3.txt/: Not a directory

This was because I tried to populate a single file that was not contained in a directory. The code expects a directory, even if it only contains 1 file, for the moment.

Missing values

Think how to treat missing values

Antibiotic and carbon source data

Improve the antibiotic and carbon source's input on the YAML file. Currently, it is only a true/false field, but we should capture much more information about it. For the moment, set it as text file that admits a small description of which antibiotic or carbon source has been used. In case of null/empty, we assume none was used.

These two papers mention both antibiotics and carbon sources:

• The role of pH in determining the species composition of the human colonic microbiota
• Enhanced butyrate formation by cross-feeding between Faecalibacterium prausnitzii and Bifidobacterium adolescentis

Standardized ways to measure growth

Consider of integrating the MCO ontology to get the various ways of measuring biomass/growth according to the review of PR #3

bacterial_growth/src/constants.py

Line 39 in bf29d8d

abundance_regex = re.compile(r'.*time.* | .*liquid.* | .*active.* | .*OD.*', flags=re.I | re.X)

Displaying tables with BR, TR or perturbation id

When the user selects the createInfoFile or plot options, the program will display (depending on the option) tables with existing studies, biological replicates, perturbations and/or technical replicates. The displayed messages should be revised. For example:

There are no perturbations with biological replicate id 101: => check for technical replicates

This message is OK if then the user is going to select a technical replicate ID (e.g., plotting option 1), bit, if plotting option is 2 (plot one set of technical replicates), the program should not go further, and, hence, that message should not have been displayed.

Serial dilutions

Introduce in the YAML file, in the biological replicate, some field that indicates whether several samples come from the same precultivation but they were serially diluted. Also, include this field in the database. It should follow this logic:

A1:A8 (biological replicate location in the plate) come from the same precultivation, but A1=d1 rate, A2=d2 rate ... A8=d8 rate (add a serial dilution rate) and serial dilution identifier XXX for the 8 BR.

Biological replicates

Change experiments for biological replicates.