Interesting links: my resume / CV (PDF format) Google Scholar NCBI My Bibliography UW Proteomics Resource Fred Hutchinson Cancer Research Center Institute for Systems Biology Fred Hutch "'Wizards' of computational science" article

email jke000 at gmail.com engj at uw.edu

helpful commands for myself:

grid engine

   qstat -j jobid | grep error              to see error message
   qmod -cj jobid                           to restart/resubmit jobs in Eqw state
   qlogin -l h=q003                                to log into a specific node, "q003" in this example
   qlogin -l mfree=1.6G -l h=q003 -pe serial 8     to log into specific node (q003), using 8 cores and 8*1.6GB RAM

git commands:

   git status
   git diff
   git add <files>
   git commit -m 'commit message'
   git push

print out column 3, a tab, then column 1 and save to a new file:

   cat somefile.txt | awk '{print $3 "\t" $1}' > newfile.txt

assume column 2 has numbers, to sum up that column:

   cat somefile.txt | awk 'BEGIN {s=0} {s=s+$2} END {print s}'

skip first line, add numbers in column 1 & 2, and separately column 2:

   more +2 somefile.txt | awk 'BEGIN {s=0; t=0} {s=s+$1+$2; t=t+$2} END {print s "\t" t} 

in-place substitution using perl:

   perl -i -pe 's/from/to/g;' -pe 's/FROM/NEW/g;' somefile.txt

my preferred source indentation formatting (Allman or ANSI/ISO C++ style with indentation size 3):

   indent -i3 -bls -bli0 -bbo -bfda -cbi0 -cli3 -cd3 -sc -nut -lp -npsl -npcs -di7 somefile.txt

pepXML Viewer peptide text regular expression:

   include string "115" and exclude peptides with G or N

   ^(?=.*115)((?!G|N).)*$

change EOL format in Vi:

   :set ff=unix
   :set ff=dos


find files without group/other read/write permission:

   find . ! -perm -g+r,-o+r

simple C strtok example:

   char *tok;
   char delims[] = "\t";  // tokenize by tab
   tok = strtok(szString, delims);
   while (tok != NULL)
   {
      printf("token '%s'\n", tok);
      tok = strtok(NULL, delims);
   }

tokenize on single character (from http://www.cplusplus.com/faq/sequences/strings/split/):

   #include <sstream>
   string s = "string, to, split";
   istringstream ss( s );
   while (!ss.eof())
   {
      string x
      getline( ss, x, ',' );
      cout << x << endl;
   }

custom strtok that doesn't skip empty tokens (from Stack Overflow):

   char *mystrtok(char **m,char *s,char c)
   {
      char *p=s?s:*m;
      if( !*p )
         return 0;
      *m=strchr(p,c);
      if( *m )
         *(*m)++=0;
      else
         *m=p+strlen(p);
      return p;
   }

   char *p, *t;

   for (t=mystrtok(&p, szBuf, ','); t ; t=mystrtok(&p, 0, ','))  // comma token
      printf("token %s\n", t);

   OR tokenize two strings at same time (which strtok does not do):

   char *p1, *t1;
   char *p2, *t2;

   for (t1=mystrtok(&p1, szBuf, ','), t2=mystrtok(&p2, szNormLine, ',') ; t1 ; t1=mystrtok(&p1, 0, ','), t2=mystrtok(&p2, 0, ','))
      printf("token %s %s\n", t1, t2);

grab specific columns in tab-delimited text file:

   cut -f1-6,8- somefile
   cut -f1,2,3,9-12,15- somefile

combine/merge multiple VOB files into one in a DOS prompt:

   copy /b vts_01_1.vob + vts_01_2.vob + vts_01_3.vob + vts_01_4.vob new.vob 

create histograms in gnuplot:

   gnuplot> binwidth = 0.01
   gnuplot> bin(x,width)=width*floor(x/width) + binwidth/2
   gnuplot> plot 'datafile.txt' using (bin($1,binwidth)):(1.0) smooth freq with boxes

valgrind to gdb thanks to ppatrick; maybe I can actually fix some bugs now:

   valgrind --leak-check=yes --db-attach=yes --db-command="/usr/bin/gdb -nw %f %p" <executable>

resubmit job in Eqw state:

   qmod -cj jobnumber

simple bash shell script to loop over input files:

   #!/bin/bash

   shopt -s nullglob

   for i in *.txt
   do
      echo "file $i"
      cat $i
   done

ffmpeg transcoding script:

   #!/bin/bash

   # test for proper usage
   if [ $# -eq 0 ] ;
   then
      echo ""
      echo " usage:  convertmp4.sh file1.avi file1.mkv"
      echo ""
      exit
   fi

   # for every argument passed on the command line
   for arg do

      echo "input: '$arg'"

      # test that the file exists and is a regular file
      if [ -f "$arg" ] ;
      then
         basename=${arg%.*}
         echo "basename: '$basename'"
         ffmpeg -i "$arg"                               -metadata title="$basename" -vcodec libx264 -acodec aac -strict -2 "$basename.mp4"
#        ffmpeg -i "$arg"                               -metadata title="$basename" -vcodec copy    -acodec copy -strict -2 "$basename.new.mp4"
#        ffmpeg -i "$arg" -vf subtitles="$basename.srt" -metadata title="$basename" -vcodec libx264 -acodec aac -strict -2 "$basename.mp4"
#        ffmpeg -i "$arg" -vf scale=720:-1 -ss 5        -metadata title="$basename" -vcodec libx264 -acodec aac -strict -2 "$basename.mp4"
      else
         echo Argument '$arg' not a regular file
         exit
      fi
   done

delete blank lines in Vi:

   :g/^$/d