   86  perl -f MPStart.pl 3 5 < Alleg_Yes.map | less
   87  perl -f MPStart.pl 2 5 < Alleg_Yes.map | less
   88  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
   89  dos2unix.exe Alleg_Yes.map 
   90  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
   91  dos2unix.exe Alleg_Yes.map 
   92  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
   93  dos2unix.exe Alleg_Yes.map 
   94  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
   95  dos2unix.exe Alleg_Yes.map 
   96  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
   97  dos2unix.exe Alleg_Yes.map 
   98  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
   99  dos2unix.exe Alleg_Yes.map 
  100  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
  101  dos2unix.exe Alleg_Yes.map 
  102  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
  103  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less | grep ^path
  104  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less | grep ^path | awk '($4 < 5){print;}'
  105  dos2unix.exe Alleg_Yes.map 
  106  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less | grep ^path | awk '($4 < 5){print;}'
  107  dos2unix.exe Alleg_Yes.map 
  108  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less | grep ^path | awk '($4 < 5){print;}'
  109  perl -f MPStart.pl 10 10 | grep oteness
  110  perl -f MPStart.pl 10 10 < Alleg_Yes.map | grep oteness
  111  perl -f MPStart.pl 10 10 < Alleg_Yes.map | less
  112  perl -f MPStart.pl 10 10 < Alleg_Yes.map | grep otness
  113  perl -f MPStart.pl 2 2 < Alleg_Yes.map | grep otness
  114  perl -f MPStart.pl 2 5 < Alleg_Yes.map | grep otness
  115  perl -f MPStart.pl 2 5 < Alleg_Yes.map | less
  116  dos2unix.exe Alleg_Yes.map
  117  perl -f MPStart.pl 2 5 < Alleg_Yes.map | less
  118  perl -f MPStart.pl 2 2 < Alleg_Yes.map | less
  119  exit
  120  cd /cygdrive/c/Program\ Files/dominions3/map
  121  cd /cygdrive/c/Program\ Files/dominions3/maps
  122  perl MPStart.pl 5 5 < Alleg_Y2.map | grep remote
  123  dos2unix.exe Alleg_Y2.map 
  124  perl MPStart.pl 5 5 < Alleg_Y2.map | grep remote
  125  perl MPStart.pl 5 5 < Alleg_Y2.map | grep path
  126  perl MPStart.pl 5 5 < Alleg_Y2.map | grep path | awk '($4 < 5){print;}'
  127  cd /cygdrive/c/Documents\ and\ Settings/Sammy/My\ Documents/
  128  ls -lrt *.csv
  129  cp Gods.csv /cygdrive/c/Program\ Files/dominions3/mods
  130  cd /cygdrive/c/Program\ Files/dominions3/
  131  cd mods
  132  ls -lrt
  133  vi GodParser.awk
  134  awk -f GodParser.awk < Gods.csv
  135  vi GodParser.awk
  136  awk -f GodParser.awk < Gods.csv
  137  vi GodParser.awk
  138  awk -f GodParser.awk < Gods.csv
  139  vi GodParser.awk
  140  awk -f GodParser.awk < Gods.csv
  141  vi GodParser.awk
  142  awk -f GodParser.awk < Gods.csv
  143  vi Gods.csv
  144  vi GodParser.awk
  145  ls -lrt
  146  dos2unix.exe 11Nations.dm 
  147  cp 11Nations.dm 11Nations_backup.txt
  148  awk -f GodParser.awk < Gods.csv >> 11Nations.dm 
  149  cp 11Nations_backup.txt 11Nations.dm
  150  vi GodParser.awk 
  151  awk -f GodParser.awk < Gods.csv >> 11Nations.dm 
  152  vi 11Nations.dm
  153  cp 11Nations_backup.txt 11Nations.dm
  154  vi GodParser.awk 
  155  cp 11Nations_backup.txt 11Nations.dm
  156  awk -f GodParser.awk < Gods.csv >> 11Nations.dm 
  157  vi 11Nations.dm 
  158  vi 11Nations.dm 
  159  vi 11Nations.dm 
  160  vi 11Nations.dm 
  161  cp 11Nations.dm 11Nations_2.bkp
  162  awk '!/#magicskill/{print; mode = 2;} /#magicskill/{print $1 " " $2 " " $3 + mode; mode = 0;}' 11Nations_2.bkp 
  163  dos2unix.exe 11Nations_2.bkp 
  164  awk '!/#magicskill/{print; mode = 2;} /#magicskill/{print $1 " " $2 " " $3 + mode; mode = 0;}' 11Nations_2.bkp | less
  165  awk '!/#magicskill/{print; if (mode > 0){print "MODE! " mode; mode = 2;} /#magicskill/{test = $3 + mode; print $1 " " $2 " " $3 + mode; mode = 0;}' 11Nations_2.bkp > 11Nations.dm
  166  vi 11Nations.dm
  167  vi 11Nations.dm
  168  awk '/--/{print ""; printf $0;} /restrictedgod/{printf " " $0;}' 11Nations
  169  awk '/--/{print ""; printf $0;} /restrictedgod/{printf " " $0;}' 11Nations.dm
  170  awk '/--/{printf $0 " ";} /restrictedgod/{print $0;}' 11Nations.dm
  171  awk '/--/{printf $0 " ";} /restrictedgod/{print $0;}' 11Nations.dm > GodList.txt
  172  vi GodList.txt 
  173  awk '/--/{printf $0 " ";} /restrictedgod/{print "," $0;}' 11Nations.dm > GodList.txt
  174  vi GodList.txt 
  175  sort -t "," -k2,2 GodList.txt 
  176  sort -t "," -k2,2 GodList.txt > GodSort.txt
  177  awk '/Dagon/{print "";} /--/{printf $0 " ";} /restrictedgod/{print "," $0;}' 11Nations.dm | sort -t "," -k2,2 > GodList.txt
  178  vi GodList.txt 
  179  awk '/Dagon/{print "";} /selectmonster/{printf $0 " ";} /--/{printf $0 " ";} /restrictedgod/{print "," $0;}' 11Nations.dm | sort -t "," -k2,2 > GodList.txt
  180  vi GodList.txt 
  181  awk '/Dagon/{print "";} /selectmonster/{printf $0 " ";} /--/{printf $0 " ";} /restrictedgod/{print "," $0;}' 11Nations.dm | sort -t "," -k2,2 > GodList.txt
  182  vi GodList.txt 
  183  scp skh2003@structure.bio.columbia.edu:/data/skh2003/NYCOMPS/Upshot.zip ./
  184  exit
  185  mv Upshot.zip /cygdrive/c/
  186  cd /cygdrive/c/Documents\ and\ Settings/Sammy
  187  cd My\ Documents/
  188  scp NYCOMPS_WTFTHISIS.csv skh2003@structure.bio.columbia.edu:/data/skh2003/NYCOMPS/
  189  scp skh2003@structure.bio.columbia.edu:/data/skh2003/NYCOMPS/NYCOMPS_WTFTHISIS3.csv ./
  190  jobs
  191  exit
  192  cd /cygdrive/c/Program\ Files/dominions3/
  193  ls -lrt
  194  cd maps
  195  ls -lrt
  196  vi Epic2C2.mp 
  197  awk '/^#Terrain/{print;}' Epic2C2.mp 
  198  dos2unix.exe Epic2C2.mp
  199  awk '/^#Terrain/{print;}' Epic2C2.mp 
  200  vi Epic2C2.mp 
  201  awk '/^#terrain/{print;}' Epic2C2.mp 
  202  awk '/^#terrain/{j = $2; if ($2 % 128 >= 64){j+=192;} print $0 " " $1 " " j;}' Epic2C2.mp 
  203  awk '/^#terrain/{j = $2; if ($2 % 128 >= 64){j+=192;} print $1 " " $2 " " j;}' Epic2C2.mp 
  204  awk '/^#terrain/{j = $3; if ($2 % 128 >= 64){j+=192;} print $1 " " $2 " " j;}' Epic2C2.mp 
  205  awk '/^#terrain/{j = $3; if ($2 % 128 >= 64){j+=192;} print $1 " " $2 " " j;}' Epic2C2.mp > Epic2c2.txt
  206  awk '/^#terrain/{j = $3; if ($2 % 128 >= 64){print;}' Epic2C2.mp
  207  awk '/^#terrain/{j = $3; if ($3 % 128 >= 64){j+=192;} print $1 " " $2 " " j;}' Epic2C2.mp > Epic2c2.txt
  208  exit
  209  cd /cygdrive/c/Program\ Files/dominions3/maps
  210  ls -lrt *.pl
  211  ls -lrt *.amp
  212  ls -lrt *.map
  213  dos2unix.exe Epic2C.map 
  214  perl MPStart.pl 5 3 < Epic2C.map > Epic2C_check.txt
  215  vi Epic2C_check.txt 
  216  grep #start Epic2C_check.txt >> Epic2C.map
  217  grep "#start" Epic2C_check.txt >> Epic2C.map
  218  vi Epic2C.map 
  219  exit
  220  cd /cygdrive/c/Documents\ and\ Settings/Sammy/My\ Documents/df_27_169_33a
  221  cd data
  222  cd save
  223  cd region1
  224  ls -lrt
  225  hexedit feature-14-8.dat
  226  hexedit world.sav
  227  exit
  228  cd /cygdrive/c
  229  scp skh2003@structure.bio.columbia.edu:/data/mingking13/STAPCOVE/proteins/AnlmaA56416372/1D7A_20.ctd ./1D7A_20_a.ctd
  230  scp skh2003@structure.bio.columbia.edu:/data/mingking13/STAPCOVE/proteins/SaotyA16759509/1D7A_20.ctd ./1D7A_20_b.ctd
  231  exit
  232  cd /cygdrive/c/Program\ Files/dominions3/
  233  cp dom3.exe dom3_hex.hex
  234  hexedit.exe dom3_hex.hex 
  235  vi events.hex 
  236  mv events.hex events.txt
  237  exit
  238  cd /cygdrive/f
  239  scp skh2003@structure.bio.columbia.edu:/data/skh2003/biocyc/BioCyc_Complex3.csv ./
  240  grep \.arc BioCyc_Complex3.csv 
  241  grep \.arc BioCyc_Complex3.csv | wc -l
  242  exit
  243  cd /cygdrive/c
  244  scp skh2003@structure.bio.columbia.edu:~/putHalT.csv ./
  245  scp skh2003@structure.bio.columbia.edu:~/HalT_sequence/HalT_brief_form.csv ./
  246  exit
  247  cd /cygdrive/c/Program\ Files/dominions3/mods
  248  ls -lrt *.dm
  249  vi 11Nations.dm 
  250  grep "^--" 11Nations.dm 
  251  grep "^--" 11Nations.dm  | grep -v "Give this"
  252  grep "^--" 11Nations.dm  | grep -v "Give this" | less
  253  cp 11Nations.dm GodsTest.dm
  254  vi GodsTest.dm 
  255  vi GodsTest.dm 
  256  grep "^--" 11Nations.dm  | grep -v "Give this" > GodList.csv
  257  vi 11Nations.dm 
  258  exit
  259  cd /cygdrive/c/Program\ Files/dominions3/
  260  cd maps
  261  ls -lrt
  262  scp blitz53.rgb skh2003@cunix.cc.columbia.edu
  263  ssh cunix.cc.columbia.edu
  264  ssh skh2003@cunix.cc.columbia.edu
  265  scp blitz53.rgb skh2003@cunix.cc.columbia.edu:~skh2003/public_html
  266  ssh skh2003@cunix.cc.columbia.edu
  267  exit
  268  cd Docs
  269  cd /cygdrive/c/Documents\ and\ Settings/Sammy/
  270  cd My\ Documents/
  271  cd My\ Pictures/
  272  cd bugs/
  273  ls -lrt
  274  scp giant-beetle.jpg skh2003@cunix.cc.columbia.edu:/~skh2003/public_html
  275  scp giant-beetle.jpg skh2003@cunix.cc.columbia.edu:~skh2003/public_html/beetle.jpg
  276  scp bugrom_base.png skh2003@cunix.cc.columbia.edu:~skh2003/public_html/bugrom_base.png
  277  ls -lrt
  278  scp bugrom_base1.png skh2003@cunix.cc.columbia.edu:~skh2003/public_html/bugrom_base.png
  279  cd /cygdrive/c
  280  scp skh2003@structure.bio.columbia.edu:/data/skh2003/CRSH_2006/OverlTable_1.csv ./
  281  scp skh2003@structure.bio.columbia.edu:/data/skh2003/CRSH_2006/KeywordTable.csv ./
  282  scp skh2003@structure.bio.columbia.edu:/data/skh2003/CRSH_2006/KeywordTable.csv ./
  283  scp skh2003@structure.bio.columbia.edu:/data/skh2003/NESG/biocyc_map.csv ./
  284  scp skh2003@structure.bio.columbia.edu:/data/skh2003/biocyc/BioCyc_Complex3.csv ./
  285  scp skh2003@structure.bio.columbia.edu:/data/skh2003/biocyc/BioCyc_Complex2.csv ./
  286  exit
  287  cd /cygdrive/c
  288  ls -lrt *.csv
  289  head BioCyc_Complex2.csv 
  290  head biocyc_map.csv 
  291  head OverlTable_1.csv 
  292  awk 'BEGIN{FS=",";} 
  293  vi biocyc_map.csv 
  294  ls -lrt *.csv
  295  vi biocyc_map.csv 
  296  exit
  297  cd /cygdrive/c
  298  ls -lrt *.csv
  299  head biocyc_map.csv 
  300  cp biocyc_map.csv map_test.csv
  301  grep ECOLI biocyc_map.csv > map_test.csv
  302  vi BioCyc_Complex2.csv map_test.csv 
  303  begin '{FS=";";} {for (i=1;i<=NF;i++){print $NF;}' map_test.csv > map_test2.csv
  304  awk 'begin {FS=";";} {for (i=1;i<=NF;i++){print $NF;}' map_test.csv > map_test2.csv
  305  awk 'begin {FS=";";} {for (i=1;i<=NF;i++){print $NF;}}' map_test.csv > map_test2.csv
  306  vi map_test2.csv 
  307  vi map_test.csv 
  308  awk 'BEGIN{FS=";";} {for (i=1;i<=NF;i++){print $NF;}}' map_test.csv > map_test2.csv
  309  vi map_test2.csv 
  310  vi map_test2.csv 
  311  awk 'BEGIN{FS=";";} {for (i=1;i<=NF;i++){print $i;}}' map_test.csv > map_test2.csv
  312  vi map_test2.csv 
  313  awk 'BEGIN{FS="=";} /ECOLI/{print $NF;}' map_test2.csv 
  314  awk 'BEGIN{FS="=";} /arc$/{printf $0 ",";} /ECOLI/{print $NF;}' map_test2.csv 
  315  vi map_test2.csv 
  316  awk 'BEGIN{FS="=";} /arc,/{printf $0 ",";} /ECOLI/{print $NF;}' map_test2.csv 
  317  awk 'BEGIN{FS="=";} /arc,/{printf $0;} /ECOLI/{print $NF;}' map_test2.csv 
  318  awk 'BEGIN{FS="=";} /arc,/{printf $0;} /ECOLI/{print $NF;}' map_test2.csv  | awk 'BEGIN{FS=",";} (NF == 3){print;}'
  319  awk 'BEGIN{FS="=";} /arc,/{printf $0;} /ECOLI/{print $NF;}' map_test2.csv  | awk 'BEGIN{FS=",";} (NF == 3){print;}' > map_test3.csv
  320  ls -lrt
  321  ls -lrt *.csv
  322  head OverlTable_1.csv 
  323  vi map_test3.csv 
  324  vi map_test2.csv 
  325  ls -lrt
  326  ls -lrt *.csv
  327  vi map_test3.csv 
  328  vi map_test3.csv 
  329  head OverlTable_1.csv 
  330  awk 'BEGIN{FS=",";} (ARGIND==1){key[$2] = $3;}'
  331  ls -lrt *.csv
  332  awk 'BEGIN{FS=",";} (ARGIND==1){key[$2] = $3;} (ARGIND==2 && key[$1] != "" && key[$2] != ""){print $0 "," key[$1] "," key[$2];}' map_test3.csv OverlTable_1.csv 
  333  awk 'BEGIN{FS=",";} (ARGIND==1){key[$2] = $3;} (ARGIND==2 && key[$1] != "" && key[$2] != ""){print $0 "," key[$1] "," key[$2];}' map_test3.csv OverlTable_1.csv > EcoCyc_CosegTest.csv &
  334  wc -l EcoCyc_CosegTest.csv 
  335  wc -l EcoCyc_CosegTest.csv 
  336  vi EcoCyc_CosegTest.csv 
  337  head EcoCyc_CosegTest.csv 
  338  ls -lrt
  339  ls -lrt *.csv
  340  vi BioCyc_Complex2.csv 
  341  awk 'BEGIN{FS=",";} (ARGIND==1){for (i=2;i<=NF;i++){seen[$i] = 2;} (ARGIND==2 && seen[$NF-1] == 2 && seen[$NF] == 2){print;}' biocyc_map.csv EcoCyc_CosegTest.csv 
  342  awk 'BEGIN{FS=",";} (ARGIND==1){for (i=2;i<=NF;i++){seen[$i] = 2;}} (ARGIND==2 && seen[$NF-1] == 2 && seen[$NF] == 2){print;}' biocyc_map.csv EcoCyc_CosegTest.csv 
  343  head EcoCyc_CosegTest.csv 
  344  ls -lrt
  345  ls -lrt *.csv
  346  head biocyc_map.csv 
  347  awk 'BEGIN{FS=",";} (ARGIND==1){for (i=2;i<=NF;i++){seen[$i] = 2;}} (ARGIND==2 && seen[$NF-1] == 2 && seen[$NF] == 2){print;}' BioCyc_Complex2.csv EcoCyc_CosegTest.csv 
  348  head BioCyc_Complex2.csv 
  349  head EcoCyc_CosegTest.csv 
  350  grep G7578 BioCyc_Complex2.csv 
  351  awk 'BEGIN{FS=",";} {print $NF-1;} {print $NF;}' BioCyc_Complex2.csv 
  352  awk 'BEGIN{FS=",";} {print $(NF-1);} {print $NF;}' BioCyc_Complex2.csv 
  353  awk 'BEGIN{FS=",";} (ARGIND==1){for (i=2;i<=NF;i++){seen[$i] = 2;}} (ARGIND==2 && seen[$(NF-1)] == 2 && seen[$NF] == 2){print;}' BioCyc_Complex2.csv EcoCyc_CosegTest.csv 
  354  awk 'BEGIN{FS=",";} (ARGIND==1){for (i=2;i<=NF;i++){seen[$i] = 2;}} (ARGIND==2 && seen[$(NF-1)] == 2 && seen[$NF] == 2){print;}' BioCyc_Complex2.csv EcoCyc_CosegTest.csv > EcoCyc_ComplexTest1.csv
  355  ls -lrt
  356  wc -l EcoCyc_ComplexTest1.csv 
  357  history > Complex_WhatIDid.txt
  358  awk 'BEGIN{FS=",";} (ARGIND==1){for (i=2;i<=NF;i++){for (j=2;j<=NF;j++){seen[$i $j] = 2; seen[$j $i] = 2;}}} (ARGIND==2){printf $0; if seen[$(NF-1) $NF] == 2{print ",YES";} else {print ",NO";}' BioCyc_Complex2.csv EcoCyc_ComplexTest1.csv > EcoCyc_ComplexTest2.csv
  359  awk 'BEGIN{FS=",";} (ARGIND==1){for (i=2;i<=NF;i++){for (j=2;j<=NF;j++){seen[$i $j] = 2; seen[$j $i] = 2;}}} (ARGIND==2){printf $0; if (seen[$(NF-1) $NF] == 2) {print ",YES";} else {print ",NO";}' BioCyc_Complex2.csv EcoCyc_ComplexTest1.csv > EcoCyc_ComplexTest2.csv
  360  awk 'BEGIN{FS=",";} (ARGIND==1){for (i=2;i<=NF;i++){for (j=2;j<=NF;j++){seen[$i $j] = 2; seen[$j $i] = 2;}}} (ARGIND==2){printf $0; if (seen[$(NF-1) $NF] == 2) {print ",YES";} else {print ",NO";}}' BioCyc_Complex2.csv EcoCyc_ComplexTest1.csv > EcoCyc_ComplexTest2.csv
  361  grep NO EcoCyc_ComplexTest2.csv 
  362  grep -c NO BioCyc_Complex2.csv 
  363  grep -c YES BioCyc_Complex2.csv 
  364  wc -l BioCyc_Complex2.csv 
  365  ls -lrt *.csv
  366  grep -c ",YES" BioCyc_ComplexTest2.csv 
  367  grep -c ",YES" EcoCyc_ComplexTest2.csv 
  368  grep -c ",NO" EcoCyc_ComplexTest2.csv 
  369  history >> Complex_WhatIDid.txt
  370  exit
  371  cd /cygdrive/c
  372  ls -lrt *.csv
  373  ls -lrt *.csv
  374  wc -l EcoCyc_ComplexTest1.csv 
  375  exit
  376  ls -lrt *.csv
  377  cd /cygdrive/c
  378  ls -lrt *.csv
  379  grep ",YeS" EcoCyc_ComplexTest2.csv 
  380  grep ",YeS" EcoCyc_ComplexTest1.csv 
  381  grep ",YES" EcoCyc_ComplexTest1.csv 
  382  vi EcoCyc_ComplexTest2.
  383  vi EcoCyc_ComplexTest2.csv 
  384  grep ",YES" EcoCyc_ComplexTest2.csv 
  385  grep ",YES" EcoCyc_ComplexTest2.csv | awk 'BEGIN{FS=",";} {print "echo COMPLEX_MEMBER_ONE";} {print "grep " $1;}'
  386  ls -lrt
  387  ls -lrt *.csv
  388  grep ",YES" EcoCyc_ComplexTest2.csv | awk 'BEGIN{FS=",";} {print "echo COMPLEX_MEMBER_ONE";} {print "grep " $1 " biocyc_map.csv"; print "echo COMPLEX_MEMBER_TWO"; print "grep " $2 " biocyc_map.csv";}' 
  389  grep ",YES" EcoCyc_ComplexTest2.csv | awk 'BEGIN{FS=",";} {print "echo COMPLEX_MEMBER_ONE";} {print "grep " $1 " biocyc_map.csv"; print "echo COMPLEX_MEMBER_TWO"; print "grep " $2 " biocyc_map.csv";}'  | csh
  390  grep ",YES" EcoCyc_ComplexTest2.csv | awk 'BEGIN{FS=",";} {print "echo COMPLEX_MEMBER_ONE";} {print "grep " $1 " biocyc_map.csv"; print "echo COMPLEX_MEMBER_TWO"; print "grep " $2 " biocyc_map.csv";}'  | csh > Complexes_Dump.txt
  391  vi Complexes_Dump.txt 
  392  exit
  393  cd /cygdrive/c
  394  scp skh2003@structure.bio.columbia.edu:/home/skh2003/NYCOMPS_targets_draft2.html ./
  395  scp skh2003@structure.bio.columbia.edu:/home/skh2003/NYCOMPS_targets_draft2.html ./
  396  scp skh2003@structure.bio.columbia.edu:/home/skh2003/NYCOMPS_targets_draft2.html ./
  397  exit
  398  cd /cygdrive/c
  399  scp skh2003@structure.bio.columbia.edu:/data/skh2003/NYCOMPS/NYCOMPS.zip
  400  scp skh2003@structure.bio.columbia.edu:/data/skh2003/NYCOMPS/NYCOMPS.zip ./
  401  exit
  402  cd /cygdrive/c
  403  scp skh2003@structure.bio.columbia.edu:/data/skh2003/NYCOMPS.zip ./
  404  scp skh2003@structure.bio.columbia.edu:/data/skh2003/NYCOMPS/NYCOMPS.zip ./
  405  ls -lrt
  406  vi for-Sam-NYCOMPS92-35.dat 
  407  awk '/^>/{print substr($1,2);}' for-Sam-NYCOMPS92-35.dat 
  408  awk '/^>/{print substr($1,2);}' for-Sam-NYCOMPS92-35.dat > Targets_WeCare.txt
  409  ls -lrt
  410  grep -f Targets_WeCare.txt NYCOMPS_int.csv
  411  grep -f Targets_WeCare.txt NYCOMPS_int_only.
  412  grep -f Targets_WeCare.txt NYCOMPS_int_only.csv 
  413  grep -f Targets_WeCare.txt NYCOMPS_int_only.csv  | wc -l
  414  grep -f Targets_WeCare.txt NYCOMPS_int_only.csv > TargetPass_Known.csv
  415  wc -l Targets_WeCare.txt 
  416  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv 
  417  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv  | sort | uniq
  418  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv  | sort | uniq | wc -l
  419  ls -lrt
  420  grep -f Targets_WeCare.txt NYCOMPS_coseg.csv > TargetPass_Pred.csv
  421  wc -l TargetPass_Pred.csv 
  422  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}' | sort | uniq | wc -l
  423  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | wc -l
  424  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq 
  425  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | awk '{print "grep -c " $1
  426  ls -lrt
  427  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | awk '{print "grep -c " $1 " Targets_WeCare.txt";}'
  428  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | awk '{print "grep -c " $1 " Targets_WeCare.txt";}' | csh
  429  vi Targets_WeCare.txt 
  430  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | awk '{print "grep -c " $1 " Targets_WeCare.txt";}'
  431  grep 331523741 Targets_WeCare.txt 
  432  vi Targets_WeCare.txt 
  433  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | awk '{print "grep -c " $1 " Targets_WeCare.txt";}' | csh
  434  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Known.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | awk '{print "grep -c " $1 " Targets_WeCare.txt";}' | csh | grep 1
  435  vi Targets_WeCare.txt 
  436  ls -lrt
  437  head Targets_WeCare.txt 
  438  awk '{print "echo -n " $1 ","; print "grep -c " $1 Targets_WeCare.txt;}'
  439  awk '{print "echo -n " $1 ","; print "grep -c " $1 "Targets_WeCare.txt";}'
  440  ls -lrt
  441  awk '{print "echo -n " $1 ","; print "grep -c " $1 "TargetPass_Known.csv";}' Targets_WeCare.txt 
  442  awk '{print "echo -n " $1 ","; print "grep -c " $1 " TargetPass_Known.csv";}' Targets_WeCare.txt 
  443  awk '{print "echo -n " $1 ","; print "grep -c " $1 " TargetPass_Known.csv";}' Targets_WeCare.txt  | csh
  444  awk '{print "echo -n " $1 ","; print "grep -c " $1 " TargetPass_Known.csv";}' Targets_WeCare.txt  | csh | grep ",1"
  445  grep 16129560 TargetPass_Known.csv 
  446  grep P0AB67 TargetPass_Known.csv 
  447  awk 'BEGIN{FS=",";} {print $2;}' TargetPass_Pred.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | awk '{print "grep -c " $1 " Targets_WeCare.txt";}' | csh | grep 1
  448  ls -lrt
  449  vi Targets_WeCare.txt 
  450  vi TargetPass_Known.csv 
  451  awk 'BEGIN{FS=",";} {print $2;}' NYCOMPS_coseg.csv | awk '{for (i=1;i<=NF;i++){print $i;}}' | sort | uniq | awk '{print "grep -c " $1 " Targets_WeCare.txt";}'
  452  ls -lrt
  453  vi for-Sam-NYCOMPS92-35.dat 
  454  zip foobar.zip for-Sam-NYCOMPS92-35.dat Targets_WeCare.txt TargetPass_Known.csv TargetPass_Pred.csv 
  455  scp foobar.zip skh2003@structure.bio.columbia.edu:~/foobar.zip
  456  exit
  457  scp skh2003@structure.bio.columbia.edu:~skh2003/Jan08.html ./
  458  scp skh2003@structure.bio.columbia.edu:~skh2003/seca_vphi.zip ./
  459  pwd
  460  mv Jan08.html seca_vphi.zip /cygdrive/c
  461  scp skh2003@structure.bio.columbia.edu:~skh2003/Jan08.html ./
  462  mv Jan08.html seca_vphi.zip /cygdrive/c
  463  exit
  464  cd /cygdrive/c/Program\ Files/dominions3/maps
  465  ls -lrt
  466  scp blitz204.rgb skh2003@structure.bio.columbia.edu:public_html
  467  scp blitz204.rgb skh2003@cunix.cc.columbia.edu:public_html/blitz204.rgb
  468  exit
  469  cd /cygdrive/c/Program\ Files/
  470  cd BlackIsle/
  471  cd Fallout2/
  472  ls
  473  cd data
  474  dir
  475  ls -lrt
  476  cd SAVEGAME/
  477  ls -lrt
  478  cd SLOT01
  479  ls -lrt
  480  hexedit.exe SAVE.DAT 
  481  exit
  482  cd /cygdrive/c/Documents\ and\ Settings/Sammy/UserData/
  483  ls -lrt
  484  cd /cygdrive/c
  485  find . --name=*.html
  486  find . name=*.html
  487  find . "name=*.html"
  488  pwd
  489  man find
  490  find . -name *.html
  491  find . --name *.html
  492  find -r . -name *.html
  493  find -R . -name *.html
  494  man find
  495  find ./ -name *.html
  496  man find
  497  find ./ -name *.html -printf
  498  find ./ -name *.html -print
  499  man find
  500  exit
  501  man awk
  502  echo foo > foo
  503  cp "foo" "foo2"
  504  vi foo2
  505  cd /cygdrive/c/Program\ Files/dominions3/mods/mixtest/
  506  unzip *.zip
  507  unzip 472982-dom3_mod_kharamdzu.zip 
  508  ls
  509  unzip 473279-Horror.zip 
  510  ls -lrt
  511  rm 473279-Horror.zip 
  512  rm 472982-dom3_mod_kharamdzu.zip 
  513  ls
  514  unzip 476419-Theran.zip ; rm 476419-Theran.zip 
  515  ls -lrt *.zip
  516  man unzip
  517  man unzip
  518  unzip -l 507116-haida102.zip ; rm 507116-haida102.zip 
  519  ls -lrt *.zip
  520  unzip 568221-Githzerai09.zip > /dev/null ; rm 568221-Githzerai09.zip 
  521  unzip 564609-chaos.zip > /dev/null ; rm 564609-chaos.zip 
  522  unzip 567051-Desert.zip > /dev/null ; rm 567051-Desert.zip 
  523  unzip 508743-Commonwealth.zip > /dev/null ; rm 508743-Commonwealth.zip 
  524  ls
  525  awk -f mod_mixer.awk *.dm
  526  ls -lrt
  527  ls megamod/*
  528  awk -f mod_mixer.awk *.dm
  529  ls -lrt
  530  cat headers.txt spells.txt weapons.txt armors.txt monsters.txt sites.txt nations.txt footers.txt > megamod.dm
  531  vi megamod.dm 
  532  awk -f mod_mixer.awk *.dm
  533  rm megamod.dm
  534  rm *.txt
  535  rm megamod/*
  536  awk -f mod_mixer.awk *.dm
  537  ls -lrt
  538  cat headers.txt spells.txt weapons.txt armors.txt monsters.txt sites.txt nations.txt footers.txt > megamod.dm
  539  ls megamod.dm
  540  grep nametype megamod.dm
  541  grep nametype megamod.dm | sort | uniq
  542  rm *.txt
  543  rm megamod.dm
  544  rm megamod/*
  545  awk -f mod_mixer.awk *.dm
  546  cat headers.txt spells.txt weapons.txt armors.txt names.txt monsters.txt sites.txt nations.txt > megamod.dm
  547  rm megamod.dm
  548  rm megamod/*
  549  rm *.txt
  550  awk -f mod_mixer.awk *.dm
  551  cat headers.txt spells.txt weapons.txt armors.txt names.txt monsters.txt sites.txt nations.txt > megamod.dm
  552  cd ..
  553  grep nametype megamod.dm
  554  grep nametype megamod.dm | sort | uniq
  555  grep -v nametype megamod.dm 
  556  grep -v nametype megamod.dm > new_megamod.dm
  557  mv new_megamod.dm megamod.dm
  558  pwd
  559  vi megamod.dm
  560  pwd
  561  cd working_late/
  562  ls
  563  ls .zip | awk '{print "unzip " $1; print "rm " $1;}'
  564  ls .zip | awk '{print "unzip " $1; print "rm " $1;}'
  565  ls *.zip | awk '{print "unzip " $1; print "rm " $1;}'
  566  ls *.zip | awk '{print "unzip " $1; print "rm " $1;}' | csh
  567  cp ../mixtest/mod_mixer.awk ./
  568  awk -f mod_mixer.awk *.dm
  569  mkdir megamod
  570  rm *.txt
  571  awk -f mod_mixer.awk *.dm
  572  ls -lrt *.dm
  573  ls -lrt *.txt
  574  vi monsters.txt 
  575  grep -v nametype headers.txt spells.txt weapons.txt armors.txt monsters.txt sites.txt nations.txt > megamod_early.dm
  576  vi megamod_early
  577  vi megamod_early.dm 
  578  grep -h -v nametype headers.txt spells.txt weapons.txt armors.txt monsters.txt sites.txt nations.txt > megamod_early.dm
  579  vi megamod_early.dm 
  580  vi megamod_early.dm 
  581  mv megamod_early.dm megamod_late.dm
  582  mv megamod megamod_late
  583  vi megamod_late
  584  vi megamod_late.dm 
  585  history > build_howto.txt
