Initially forked from here. Thank you to the awesome binder team!
Part of the Bioinformatics Virtual Coordination Network :)
Enter the MagicCave
cd MagicCave/
print the MagicLamp help menu
MagicLamp.py help
print WspGenie help menu
MagicLamp.py WspGenie -h
run WspGenie on test dataset
MagicLamp.py WspGenie -bin_dir test_dataset/ -bin_ext fna -out wspgenie_out
go into the wspgenie output directory and check out the output file
cd wspgenie_out/
less -S wspgenie-summary.csv
check out the gene predictions
cd ORF_calls/
cd ../../
mv ORF calls to the main directory
mv wspgenie_out/ORF_calls/ ./
print LithoGenie help menu
MagicLamp.py LithoGenie -h
run LithoGenie on ORF calls
MagicLamp.py LithoGenie -bin_dir ORF_calls/ -bin_ext faa --orfs -out lithogenie_out
check out the output
cd lithogenie_out/
less -S lithogenie-summary.csv
less lithogenie.ALL.heatmap.csv
cd ../
re-run LithoGenie to create a .heatmap.csv for an element-of-interest
MagicLamp.py LithoGenie -bin_dir ORF_calls/ -bin_ext faa --orfs -out lithogenie_out --skip -cat sulfur
# answer 'y' to the question
MagicLamp.py LithoGenie -bin_dir ORF_calls/ -bin_ext faa --orfs -out lithogenie_out --skip -cat iron
check out the new results
cd lithogenie_out/
less lithogenie.sulfur.heatmap.csv
less lithogenie.iron.heatmap.csv
print the HmmGenie help menu
MagicLamp.py HmmGenie -h
run HmmGenie with a set of HMMs for gas vesicle formation
MagicLamp.py HmmGenie -hmm_dir MagicCave/hmms/gas/ -hmm_ext hmm -bin_dir test_dataset/ -bin_ext fna -out gas_out
check out the results and re-run HmmGenie with more stringent parameters
MagicLamp.py HmmGenie -hmm_dir MagicCave/hmms/gas/ -hmm_ext hmm -bin_dir test_dataset/ -bin_ext fna -out gas_out -clu 5
check out the results
cd gas_out/
less -S genie-summary.csv