Temp2 Method Fails with Test Data

[SColson82]

After installing conda, mamba, and mcclintock locally and downloading and running the test data as per the repository README, the test data results were found to be as follows:

METHOD          ALL       REFERENCE    NON-REFERENCE 
-----------------------------------------------------
ngs_te_mapper   35        21           14            
ngs_te_mapper2  87        49           38            
relocate        80        63           17            
relocate2       139       41           98            
temp            365       311          54            
temp2           311       311          0                    <-- large difference, unexpected
retroseq        58        0            58            
popoolationte   142       129          13              <-- small difference, expected
popoolationte2  187       163          24             <-- small difference, expected
te-locate       713       164          549           
teflon          414       390          24            
tebreak         60        0            60            
-----------------------------------------------------

There are 3 messages in output/logs/<datestamp>/temp2.log that I found to be concerning:

• /usr/bin/env: ‘python2.7’: No such file or directory
• Error in read.table(Args[8], header = F, row.names = NULL) : no lines available in input Execution halted
• ***** ERROR: Requested column 2, but database file - only has fields 1 - 0.

I found that the temp2 method uses environment at mcclintock/install/envs/conda/a44faccd and activated that environment to find that it installs with python3.10 rather than python2.7 but the temp2 software installed in mcclintock/install/tools/temp2/ contain python2 scripts. I tried several things to resolve this including: modifying the mcc_temp2.yml in mcclintock/install/envs to include python2.7 when the environment is installed, uninstalling python3.10 and installing python2.7 in the existing environment, and moving the installed temp2 method files out of the way and cloning the current Temp2 repository into that space but each of these errored.

In the end I was able to modify getTPRegion.py and processMergedBed.py which are located in mcclintock/install/tools/temp2/bin in the following manner:

1. line 17 of getTPRegion.py needs to indented only once to align with python indentation rules.
2. run 2to3 -w getTPRegion.py processMergedBed.py to modify those files to run on python3 rather than python 2.

This resulted in the following output for the temp2 data:

temp2           366       311          55   

As you can see, this is off by 1 in the first and third column. I am the research IT support and don't understand the science behind these methods so I am hoping to have you confirm that these changes result in the method working correctly and not "almost correctly". When you have the opportunity, I would appreciate your feedback on this matter.