bm2lab/idmer repository overview

`python  /home/main.py exp -VDN  VTPs_DN.tsv  -VUP  VTPs_UP.tsv  -EDN  EHFs_DN.tsv   -EUP  EHFs_UP.tsv  -output  exp`    

or  
`python  /home/main.py exp -VDN  VTPs_DN.tsv  -VUP  VTPs_UP.tsv  -EDN  EHFs_DN.tsv   -EUP  EHFs_UP.tsv  -output  expGAT  --GAT` 

In denovo mode, (1) As for the test virus' VTPs, iDMer applies HVPPI to predict them based on the test virus genome information and the candidate VTPs that may interact with the test virus. The set of union VTPs from viruses that belongs to the same family of the test virus are taken as the candidate VTPs. Subsequently, please classify the predicted VTPs as reliance or restriction genes accroding to their functions described in KEGG and Reactome Pathway Database and make a config file to indicate whether the predicted VTPs are reliance or restriction genes; (2) As for the test virus' EHFs, the set of overlapping EHFs from viruses that belongs to the same family of the test virus are taken as the test virus' EHFs. Classify the test virus' EHFs as reliance or restriction genes accroding to their functions described in KEGG and Reactome Pathway Database. Finally, run iDMer denovo mode as follows:  

   `python  /home/main.py   denovo   -EDN   EHFs_DN.tsv  -EUP  EHFs_UP.tsv  -virus  virus.fa  -host  host.fa  -config  config.tsv  -output  denovo`    
or       
   `python  /home/main.py   denovo   -EDN   EHFs_DN.tsv  -EUP  EHFs_UP.tsv  -virus  virus.fa  -host  host.fa  -config  config.tsv  -output  denovoGAT  --GAT`