astrobiomike / 2022-summer-nasa-genelab-intern-rose-carion

GL 2022 Internship

Mike Lee's GeneLab 2022 Summer Internship Wiki

HackMD Pages

First HackMD Page

GeneLab Amplicon Processing

GeneLab Metagenomics Processing

Test Dataset Metagenomics Processing Code

Annotation of Mike Lee's Metagenomics Processing Code

Code Use Instructions

To test the above codes (metagenomics_user_input_validation.py, amplicon_user_input_validation.py):

Installation:

• Install conda as described by Mike Lee

• 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/

Metagenomics Code

After running the code, the user will be asked to input data.

1. GLDS ID
   e.g. 'GLDS-276'
2. Path to the sample names file
   e.g. '/Users/rosecarion/Desktop/GL-metagenomics-output-for-validation-testing/unique-sample-IDs.txt'
3. Expected additional filename prefix that was added to the files that describe multiple samples (default is a back slash)
   Press 'return' key if none
4. 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

Amplicon Code

After running the code, the user will be asked to input data.

1. GLDS ID
   e.g. 'GLDS-276'
2. Path to the sample names file
   e.g. '/Users/rosecarion/Desktop/Amplicon_validation/GL-amplicon-output-for-validation-testing/unique-sample-IDs.txt'
3. Output file prefix if there is one
   Press 'return' key if none
4. Specify whether primers trimmed prior to GeneLab processing
   e.g. 'y' for 'yes'
   'n' for 'no'
5. 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

Code with external functions

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.