9/14/24
-------

test case for anova:

> python3 ../../transit.py anova cholesterol_glycerol_combined.dat samples_metadata_cg.txt ../genomes/H37Rv.prot_table temp

1/28/24
-------

test --ref in ZINB (for Wael)

> python3 ../../transit.py zinb cholesterol_glycerol_combined.dat samples_metadata_cg.txt ../genomes/H37Rv.prot_table temp1.txt
> python3 ../../transit.py zinb cholesterol_glycerol_combined.dat samples_metadata_cg.txt ../genomes/H37Rv.prot_table temp1b.txt --ref Cholesterol
problem! LFC does not invert (for k=2 conditions; where there is only 1 LFC)
> python3 ../../transit.py zinb cholesterol_glycerol_combined.dat temp.meta ../genomes/H37Rv.prot_table temp1c.txt
switch order of conditions in metadata file
this just switches order of Glyc vs Chol, but doesn't fix LFCs
> python3 ../../transit.py zinb cholesterol_glycerol_combined.dat temp.meta ../genomes/H37Rv.prot_table temp1d.txt --include-condtions Glycerol,Cholesterol


> python3 ../../transit.py zinb iron_combined_wig4.txt iron_samples_metadata.txt ../genomes/H37Rv.prot_table temp2.txt

> python3 ../../transit.py zinb iron_combined_wig4.txt iron_samples_metadata.txt ../genomes/H37Rv.prot_table temp3.txt --ref FeCMBT 

> python3 ../../transit.py zinb iron_combined_wig4.txt iron_samples_metadata.txt ../genomes/H37Rv.prot_table temp4.txt --ref FeCMBT --prot_table ../genomes/H37Rv.prot_table


1/9/24
------

> python3 ../../transit.py resampling glycerol_H37Rv_rep1.wig,glycerol_H37Rv_rep2.wig cholesterol_H37Rv_rep1.wig,cholesterol_H37Rv_rep2.wig,cholesterol_H37Rv_rep3.wig ../genomes/H37Rv.prot_table resampling_glyc_chol.txt -a
74 hits

SR resampling:

> python3 ../../transit.py resampling glycerol_H37Rv_rep1.wig,glycerol_H37Rv_rep2.wig cholesterol_H37Rv_rep1.wig,cholesterol_H37Rv_rep2.wig,cholesterol_H37Rv_rep3.wig ../genomes/H37Rv.prot_table resampling_glyc_chol.SR.txt -sr -a
147 hits


11/24/21
--------
Michael Y Galperin, Yuri I Wolf, Kira S Makarova, Roberto Vera Alvarez, David Landsman, Eugene V Koonin (2021).
COG database update: focus on microbial diversity, model organisms, and widespread pathogens. NAR.
https://academic.oup.com/nar/article/49/D1/D274/5964069


10/17/21
--------

extract cellular localization info as children of GO:0110165 cellular anatomical entity:
  GO:0042597 periplasmic space
  GO:0005737 cytoplasm
  GO:0071944 cell periphery
  GO:0016020 membrane
  GO:0005615 extracellular space
  and many more...

I did this us /pacific/home/ioerger/U19/



3/29/21
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made list of 53 iron-related genes for Sami Nelson (Sassetti lab)

I think I did this:

> python list_GO_terms.py > iron_related_GO_terms.txt

12/20/20
--------

got smeg_GO_terms.txt from PATRIC
4832/6716 genes have at least 1 GO term
