Wednesday, February 20, 2008

Get rid of horizontal line in Word 2007

"This line is actually... Wait for it...! A border! Don't ask me how it got there, but all you need to do is highlight the section around the line (just left mouse, and pull a nice big block round the area, provided there are no tables nearby where you want to preserve a border). Then just go up to the border-line selection icon in the toolbar and choose the one that clears all borders."
From http://word-tips-world.blogspot.com/2007/06/get-rid-of-that-annoying-horizontal.html

Tuesday, February 05, 2008

BLAST performance analysis configuration

All the files needed for BLAST performance testing (e.g., perl scripts, databases, different versions of BLAST software, ...) are located under my account on everest under ~/BLASTanalysis.
In order to run a BLAST test, a properties file (e.g., propertyFile) needs to be edited/provided. Properties file specifies the following data: database, input file, program, I/O params are specified, number of fragments and threads, and execution host.
Once configured, run run.pl script. This script will split the input file into specified number of fragments, generate LRM scripts, and submit the job:
perl run.pl {properties file}

Add multiple linux timing results (output in seconds)

If there are multiple files with timing results resulting from Linux 'time' command:
$ cat outputFile* | grep real
real 4m5.047s
real 2m51.264s
real 2m52.414s
real 2m52.293s

And these timings need to be converted into seconds and added into a single number (e.g., 761.018), use the following command:
cat outputFile* | grep real | cut -f 2 | sed 's/m/*60+/' | sed 's/s//g' | bc | awk '{ printf "%s", $0 "+" }' | sed '$s/.$/\n/' | bc

Convert output of linux 'time' command to show seconds only

After executing Linux 'time' command, the following output is obtained:
real 2m52.293s
user 1m39.670s
sys 0m4.370s

Use the following command to extract value for 'real' time only and convert the output to seconds only (i.e., convert 2m52.293s into 172.293):
cat outputFile* | grep real | cut -f 2 | sed 's/m/*60+/' | sed 's/s//g' | bc