Mike Lee's GeneLab 2022 Summer Internship Wiki
GeneLab Metagenomics Processing
Test Dataset Metagenomics Processing Code
Annotation of Mike Lee's Metagenomics Processing Code
To test the above codes (metagenomics_user_input_validation.py, amplicon_user_input_validation.py):
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Install conda as described by Mike Lee
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Install dp_tools
curl -L -o dp_tools-condaEnv.yaml https://raw.githubusercontent.com/J-81/dp_tools/main/condaEnv.yaml
conda env create -f dp_tools-condaEnv.yaml
conda activate dp_tools
- Download, unpack, and move metagenomics test data to an output directory with:
curl -L -o GL-metagenomics-output-for-validation-testing.tar.gz https://figshare.com/ndownloader/files/36039989
tar -xzvf GL-metagenomics-output-for-validation-testing.tar.gz
cd GL-metagenomics-output-for-validation-testing/
- Download, unpack, and move amplicon test data to an output directory with:
curl -L -o GL-amplicon-output-for-validation-testing.tar.gz https://figshare.com/ndownloader/files/36252156
tar -xzvf GL-amplicon-output-for-validation-testing.tar.gz
cd GL-amplicon-output-for-validation-testing/
After running the code, the user will be asked to input data.
- GLDS ID
e.g. 'GLDS-276' - Path to the sample names file
e.g. '/Users/rosecarion/Desktop/GL-metagenomics-output-for-validation-testing/unique-sample-IDs.txt' - Expected additional filename prefix that was added to the files that describe multiple samples (default is a back slash)
Press 'return' key if none - Specify whether the test data is single-ended
e.g. 'y' for 'yes'
'n' for 'no'
Information regarding the downloaded test data: GLDS ID is 'TEST', there is no expected additional filename prefix, not single-ended
After running the code, the user will be asked to input data.
- GLDS ID
e.g. 'GLDS-276' - Path to the sample names file
e.g. '/Users/rosecarion/Desktop/Amplicon_validation/GL-amplicon-output-for-validation-testing/unique-sample-IDs.txt' - Output file prefix if there is one
Press 'return' key if none - Specify whether primers trimmed prior to GeneLab processing
e.g. 'y' for 'yes'
'n' for 'no' - Specify whether the test data is single-ended
e.g. 'y' for 'yes'
'n' for 'no'
Information regarding the downloaded test data: GLDS ID is 'TEST', there is no output file prefix, primers are not trimmed, not single-ended
ex_function_metagenomics_validation.py and ex_function_amplicon_validation.py call overlapping functions from overlapping_functions_amplicon_metagenomics_validation.py
The codes with external functions can be used after downloading overlapping_functions_amplicon_metagenomics_validation.py and placing the code in the same directory as ex_function_metagenomics_validation.py and ex_function_amplicon_validation.py. The codes can be run by following the "Code Use Instructions" above.