meta-PPISP Post Handler

The following python script and library are needed to automatically submit meta-PPISP jobs for a large number of proteins and obtain predictions from your own computer.

Usage

(1) Save these 2 files in a directory on your computer. From there, to submit a meta-PPISP job, type the command:
python meta-PPISP-submit.py $1 $2 $3 $4 > $1.html

where

  • $1 = submission name. (It should be unique for each meta-PPISP job; otherwise prediction will be overwritten.)
  • $2 = your email address
  • $3 = the protein chain IDs in the PDB file on which you want to predict a protein-binding site. $3 has the format "_" or "A" or "A,B,C" and must match the chains in the PDB file.
  • $4 = PDB filename. (You can specify the full path of the file.)
  • $1.html contains information on the job submitted and a link to the prediction. To view it, simply type:
w3m $1.html

(2) Wait for the job to finish (typically a few minutes); the prediction is then sent to you by e-mail. The prediction is also displayed when you click the link in $1.html. You can save the prediction to a file, e.g., $1.out, by typing:
wget -O $1.out -F -i $1.html

(3) Combining the above two steps allows you to automatically submit multiple jobs. Copy the following lines to a file called ppisp-submit.scr:
python meta-PPISP-submit.py $1 $2 $3 $4 > $1.html
sleep 1200
wget -O $1.out -F -i $1.html
Note: "sleep 1200" is added to allow a wait period of 1200 seconds before collecting prediction and submitting a new job.

Change the mode of ppisp-submit.scr to executable (chmod +x ppisp-submit.scr), and create a run file (e.g., ppisp-submit.run) that contains one line for each protein. The run file looks like this:
./ppisp-submit.scr job1 email chain1 pdb1
./ppisp-submit.scr job2 email chain2 pdb2
etc. Change the mode of the run file to executable and then type the name of the run file. The predictions will be saved in job1.out, job2,out, etc.


http://pipe.scs.fsu.edu