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How do I save scores from Pileup runs ?

When you run Pileup interactively, it prints the pairwise similarity scores to the screen. You see output like this:
Determining pairwise similarity scores...
     
        1   x     2       1.19
        1   x     3       1.20
     
      ////////////////////////
     
       26   x    28       0.87
       27   x    28       0.86
However, the final output file does not contain these scores. If you want to save or print the scores, the quick-and-dirty way is to cut-and-paste them from your screen into a file. An alternative way is to run pileup in batch mode with the '-monitor' option. Since pileup runs can be long, batch mode may be a good idea anyway. When the batch job is done, it will send mail to your account, and if you have the '-monitor' flag, the mail will contain the pairwise scores.

Sample session:
% pileup -batch -monitor

PileUp creates a multiple sequence alignment from a group of related
sequences using progressive, pairwise alignments.  It can also plot a
tree showing the clustering relationships used to create the alignment. 

 PileUp of what sequences ?  @hsp2.list


   1         BBHSP60  1931 bp
   2         BBHSPRO  2116 bp
   3        BBOSPAGE   819 bp

 What is the gap creation penalty (* 5.00 *) ?  

 What is the gap extension penalty (* 0.30 *) ?  

 The minimum density for a one-page plot is 3.3 sequences/100 platen units.
 What density do you want (* 3.3 *) ?  

 What should I call the output file name (* hsp2.msf *) ? 

 ** pileup will run as a batch or at job.

 ** pileup was submitted using the command:
    "  atnow  "

warning: commands will be executed using /bin/sh
job 865448280.a at Wed Jun  4 14:18:00 1997

Mail received when batch job finishes:
Date: Wed, 4 Jun 1997 14:18:23 -0400 (EDT)
From: Susan Chacko <susanc@helix.nih.gov>
Subject: pileup

                     Welcome to the WISCONSIN PACKAGE 
                      Version 8.1-UNIX, August 1995
			[....etc....]
Running pileup using :
..
-monitor
-INfile1=@hsp2.list
-GAPweight=5.000000
-LENgthweight=0.300000
-OUTfile1=hsp2.msf
-DENsity=3.333433
-FIGure
-Default

   1         BBHSP60  1931 bp
   2         BBHSPRO  2116 bp
   3        BBOSPAGE   819 bp

 Determining pairwise similarity scores...

   1   x     2       0.36
   1   x     3       0.37
   2   x     3       0.38

 Aligning...

   1     ........................................-.....
   2     ..................................................
         ..............................................-...
         .......


        Total sequences:          3
       Alignment length:      2,120
               CPU time:      09.97

            Output file:/u5/susanc/hsp2.msf