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tan0101 / MGS_ISME2022

"Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock" by Alexandre Maciel-Guerra, Michelle Baker, Yue Hu, Wei Wang, Xibin Zhang, Jia Rong, Yimin Zhang, Jing Zhang, Jasmeet Kaler, David Renney, Matthew Loose, Richard D Emes, Longhai Liu, Junshi Chen, Zixin Peng, Fengqin Li, and Tania Dottorini
GNU Affero General Public License v3.0
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Instructions and sample data #1

Open raqueldias opened 2 years ago

raqueldias commented 2 years ago

Hi, I came across your article recently and I was really interested in understanding the methods you used to generate Figure 6. I was trying to run your script on my data but I have no clue of how the input file should look like. What format and what columns is your script expecting to receive as input? would you have one example of input data, or the input file that you used with this script for the article?

innovatekdd commented 2 years ago

Hi, I came across your article recently and I was really interested in understanding the methods you used to generate Figure 6. I was trying to run your script on my data but I have no clue of how the input file should look like. What format and what columns is your script expecting to receive as input? would you have one example of input data, or the input file that you used with this script for the article?

Dear Raquel,

Thank you for reading our paper and trying to execute the files. In both scripts the main files you need will be: 1. "data_MGS" which in our case we have used the resistome data from the metagenomics, which has in the columns the presence/absence of the different genes and on the rows the samples; 2. "antibiotic_df" which is the Resistant/Susceptible/Intermediate AMR pattern, so each row represent a sample and each column an antibiotic.; 3. "metadata_df" which has in the rows the samples, and in our case on the columns the humidity/temperature value for each sample.

The script FrameworkFigure6A.py will create a csv file with the selected features, this file will then be used as input for the script FrameworkFigure6B.py, since it will only analyse with the regression the features that were important for the classification.

In case you need any help please don't hesitate to contact us again.

Best regards,

Alexandre Maciel Guerra

raqueldias commented 2 years ago

Thanks for the prompt response and for all the detailed information! It makes more sense now.