WESA Post Handler

The following python script and library are needed to automatically submit WESA 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 WESA job, type the command:
python WESA-submit.py $1 $2 $3 > $1.html

where

  • $1 = submission name. (It should be unique for each WESA job; otherwise prediction will be overwritten.)
  • $2 = your email address
  • $3 = sequence 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 wesa-submit.scr:
python WESA-submit.py $1 $2 $3 > $1.html
sleep 900
wget -O $1.out -F -i $1.html
Note: "sleep 900" is added to allow a wait period of 900 seconds before collecting prediction and submitting a new job.

Change the mode of wesa-submit.scr to executable (chmod +x wesa-submit.scr), and create a run file (e.g., wesa-submit.run) that contains one line for each protein. The run file looks like this:
./wesa-submit.scr job1 email seq1
./wesa-submit.scr job2 email seq2
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.


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