%!PS-Adobe-3.0
%%Title: GP3xCLI.awk
%%For: Tony Reverter-Gomez
%%Creator: a2ps version 4.13
%%CreationDate: Sun Jan 29 20:46:33 2006
%%BoundingBox: 24 24 588 768
%%DocumentData: Clean7Bit
%%Orientation: Portrait
%%Pages: 5
%%PageOrder: Ascend
%%DocumentMedia: Letter 612 792 0 () ()
%%DocumentNeededResources: font Courier
%%+ font Courier-Bold
%%+ font Courier-BoldOblique
%%+ font Courier-Oblique
%%+ font Helvetica
%%+ font Helvetica-Bold
%%+ font Symbol
%%+ font Times-Bold
%%+ font Times-Roman
%%DocumentProcessColors: Black 
%%DocumentSuppliedResources: procset a2ps-a2ps-hdr
%%+ procset a2ps-black+white-Prolog
%%+ encoding ISO-8859-1Encoding
%%EndComments
/a2psdict 200 dict def
a2psdict begin
%%BeginProlog
%%Copyright: (c) 1988, 89, 90, 91, 92, 93 Miguel Santana
%%Copyright: (c) 1995, 96, 97, 98 Akim Demaille, Miguel Santana
% Check PostScript language level.
/languagelevel where {
  pop /gs_languagelevel languagelevel def
} {
  /gs_languagelevel 1 def
} ifelse

% EPSF import as in the Red Book
/BeginInclude {
  /b4_Inc_state save def    		% Save state for cleanup
  /dict_count countdictstack def	% Count objects on dict stack
  /op_count count 1 sub def		% Count objects on operand stack 
  userdict begin
    0 setgray 0 setlinecap
    1 setlinewidth 0 setlinejoin
    10 setmiterlimit [ ] 0 setdash newpath
    gs_languagelevel 1 ne {
      false setstrokeadjust false setoverprint 
    } if
} bind def

/EndInclude {
  count op_count sub { pos } repeat	% Clean up stacks
  countdictstack dict_count sub { end } repeat
  b4_Inc_state restore
} bind def

/BeginEPSF {
  BeginInclude
  /showpage { } def
} bind def

/EndEPSF {
  EndInclude
} bind def

% Page prefeed
/page_prefeed {         % bool -> -
  statusdict /prefeed known {
    statusdict exch /prefeed exch put
  } {
    pop
  } ifelse
} bind def

/deffont {
  findfont exch scalefont def
} bind def

/reencode_font {
  findfont reencode 2 copy definefont pop def
} bind def

% Function c-show (str => -)
% centers text only according to x axis.
/c-show { 
  dup stringwidth pop
  2 div neg 0 rmoveto
  show
} bind def

% Function l-show (str => -)
% prints texts so that it ends at currentpoint
/l-show {
  dup stringwidth pop neg 
  0 
  rmoveto show
} bind def

% center-fit show (str w => -)
% show centered, and scale currentfont so that the width is less than w
/cfshow {
  exch dup stringwidth pop
  % If the title is too big, try to make it smaller
  3 2 roll 2 copy
  gt
  { % if, i.e. too big
    exch div
    currentfont exch scalefont setfont
  } { % ifelse
    pop pop 
  }
  ifelse
  c-show			% center title
} bind def

% Return the y size of the current font
% - => fontsize
/currentfontsize {
  currentfont /FontType get 0 eq {
    currentfont /FontMatrix get 3 get
  }{
    currentfont /FontMatrix get 3 get 1000 mul
  } ifelse
} bind def

% reencode the font
% <encoding-vector> <fontdict> -> <newfontdict>
/reencode { %def
  dup length 5 add dict begin
    { %forall
      1 index /FID ne 
      { def }{ pop pop } ifelse
    } forall
    /Encoding exch def

    % Use the font's bounding box to determine the ascent, descent,
    % and overall height; don't forget that these values have to be
    % transformed using the font's matrix.
    % We use `load' because sometimes BBox is executable, sometimes not.
    % Since we need 4 numbers an not an array avoid BBox from being executed
    /FontBBox load aload pop
    FontMatrix transform /Ascent exch def pop
    FontMatrix transform /Descent exch def pop
    /FontHeight Ascent Descent sub def

    % Define these in case they're not in the FontInfo (also, here
    % they're easier to get to.
    /UnderlinePosition 1 def
    /UnderlineThickness 1 def
    
    % Get the underline position and thickness if they're defined.
    currentdict /FontInfo known {
      FontInfo
      
      dup /UnderlinePosition known {
	dup /UnderlinePosition get
	0 exch FontMatrix transform exch pop
	/UnderlinePosition exch def
      } if
      
      dup /UnderlineThickness known {
	/UnderlineThickness get
	0 exch FontMatrix transform exch pop
	/UnderlineThickness exch def
      } if
      
    } if
    currentdict 
  end 
} bind def

% composite fonts for ASCII-EUC mixed string
% Version 1.2 1/31/1990
% Orignal Ken'ichi HANDA (handa@etl.go.jp)
% Modified Norio Katayama (katayama@rd.nacsis.ac.jp),1998
% Extend & Fix Koji Nakamaru (maru@on.cs.keio.ac.jp), 1999
% Anyone can freely copy, modify, distribute this program.

/copyfont {	% font-dic extra-entry-count  copyfont  font-dic
	1 index maxlength add dict begin
	{	1 index /FID ne 2 index /UniqueID ne and
		{def} {pop pop} ifelse
	} forall
	currentdict
	end
} bind def

/compositefont { % ASCIIFontName EUCFontName RomanScale RomanOffset Rot(T/F) compositefont font
    /RomanRotation exch def
    /RomanOffset exch def
    /RomanScale exch def
    userdict /fixeucfont_dict known not {
	userdict begin
	    /fixeucfont_dict 2 dict begin
		/UpperByteEncoding [
		    16#00 1 16#20 { pop 0 } for
		    16#21 1 16#28 { 16#20 sub } for
		    16#29 1 16#2F { pop 0 } for
		    16#30 1 16#74 { 16#27 sub } for
		    16#75 1 16#FF { pop 0 } for
		] def
	        /LowerByteEncoding [
		    16#00 1 16#A0 { pop /.notdef } for
		    16#A1 1 16#FE { 16#80 sub 16 2 string cvrs
				    (cXX) dup 1 4 -1 roll
				    putinterval cvn } for
		    /.notdef
		] def
		currentdict
	    end def
	end
    } if
    findfont dup /FontType get 0 eq {
	14 dict begin
	    %
	    % 7+8 bit EUC font
	    %
	    12 dict begin
		/EUCFont exch def
		/FontInfo (7+8 bit EUC font) readonly def
		/PaintType 0 def
		/FontType 0 def
		/FontMatrix matrix def
		% /FontName
		/Encoding fixeucfont_dict /UpperByteEncoding get def
		/FMapType 2 def
		EUCFont /WMode known
		{ EUCFont /WMode get /WMode exch def }
		{ /WMode 0 def } ifelse
		/FDepVector [
		    EUCFont /FDepVector get 0 get
		    [ 16#21 1 16#28 {} for 16#30 1 16#74 {} for ]
		    {
			13 dict begin
			    /EUCFont EUCFont def
			    /UpperByte exch 16#80 add def	
			    % /FontName
			    /FontInfo (EUC lower byte font) readonly def
			    /PaintType 0 def
			    /FontType 3 def
			    /FontMatrix matrix def
			    /FontBBox {0 0 0 0} def
			    /Encoding
				fixeucfont_dict /LowerByteEncoding get def
			    % /UniqueID
			    % /WMode
			    /BuildChar {
				gsave
				exch dup /EUCFont get setfont
				/UpperByte get
				2 string
				dup 0 4 -1 roll put
				dup 1 4 -1 roll put
				dup stringwidth setcharwidth
				0 0 moveto show
				grestore
			    } bind def
			    currentdict
			end
			/lowerbytefont exch definefont
		    } forall
		] def
		currentdict
	    end
	    /eucfont exch definefont
	    exch
	    findfont 1 copyfont dup begin
		RomanRotation {
			/FontMatrix FontMatrix
			[ 0 RomanScale neg RomanScale 0 RomanOffset neg 0 ]
			matrix concatmatrix def
		}{
			/FontMatrix FontMatrix
			[ RomanScale 0 0 RomanScale 0 RomanOffset ] matrix concatmatrix
			def
			/CDevProc
			    {pop pop pop pop 0 exch -1000 exch 2 div 880} def
		} ifelse
	    end
	    /asciifont exch definefont
	    exch
	    /FDepVector [ 4 2 roll ] def
	    /FontType 0 def
	    /WMode 0 def
	    /FMapType 4 def
	    /FontMatrix matrix def
	    /Encoding [0 1] def
	    /FontBBox {0 0 0 0} def
%	    /FontHeight 1.0 def % XXXX
	    /FontHeight RomanScale 1.0 ge { RomanScale }{ 1.0 } ifelse def
	    /Descent -0.3 def   % XXXX
	    currentdict
	end
	/tmpfont exch definefont
	pop
	/tmpfont findfont
    }{
	pop findfont 0 copyfont
    } ifelse
} def	

/slantfont {	% FontName slant-degree  slantfont  font'
    exch findfont 1 copyfont begin
    [ 1 0 4 -1 roll 1 0 0 ] FontMatrix exch matrix concatmatrix
    /FontMatrix exch def
    currentdict
    end
} def

% Function print line number (<string> # -)
/# {
  gsave
    sx cw mul neg 2 div 0 rmoveto
    f# setfont
    c-show
  grestore
} bind def

% -------- Some routines to enlight plain b/w printings ---------

% Underline
% width --
/dounderline {
  currentpoint
  gsave
    moveto
    0 currentfont /Descent get currentfontsize mul rmoveto
    0 rlineto
    stroke
  grestore
} bind def

% Underline a string
% string --
/dounderlinestring {
  stringwidth pop
  dounderline
} bind def

/UL {
  /ul exch store
} bind def

% Draw a box of WIDTH wrt current font
% width --
/dobox {
  currentpoint
  gsave
    newpath
    moveto
    0 currentfont /Descent get currentfontsize mul rmoveto
    dup 0 rlineto
    0 currentfont /FontHeight get currentfontsize mul rlineto
    neg 0 rlineto
    closepath
    stroke
  grestore
} bind def

/BX {
  /bx exch store
} bind def

% Box a string
% string --
/doboxstring {
  stringwidth pop
  dobox
} bind def

%
% ------------- Color routines ---------------
%
/FG /setrgbcolor load def

% Draw the background
% width --
/dobackground {
  currentpoint
  gsave
    newpath
    moveto
    0 currentfont /Descent get currentfontsize mul rmoveto
    dup 0 rlineto
    0 currentfont /FontHeight get currentfontsize mul rlineto
    neg 0 rlineto
    closepath
    bgcolor aload pop setrgbcolor
    fill
  grestore
} bind def

% Draw bg for a string
% string --
/dobackgroundstring {
  stringwidth pop
  dobackground
} bind def


/BG {
  dup /bg exch store
  { mark 4 1 roll ] /bgcolor exch store } if
} bind def


/Show {
  bg { dup dobackgroundstring } if
  ul { dup dounderlinestring } if
  bx { dup doboxstring } if
  show
} bind def

% Function T(ab), jumps to the n-th tabulation in the current line
/T {
  cw mul x0 add
  bg { dup currentpoint pop sub dobackground } if
  ul { dup currentpoint pop sub dounderline } if
  bx { dup currentpoint pop sub dobox } if
  y0 moveto
} bind def

% Function n: move to the next line
/n {
  /y0 y0 bfs sub store
  x0 y0 moveto
} bind def

% Function N: show and move to the next line
/N {
  Show
  /y0 y0 bfs sub store
  x0 y0 moveto
} bind def

/S {
  Show
} bind def

%%BeginResource: procset a2ps-a2ps-hdr 2.0 2
%%Copyright: (c) 1988, 89, 90, 91, 92, 93 Miguel Santana
%%Copyright: (c) 1995, 96, 97, 98 Akim Demaille, Miguel Santana
% Function title: prints page header.
% <ct> <rt> <lt> are passed as argument
/title { 
  % 1. Draw the background
  x v get y v get moveto
  gsave
    0 th 2 div neg rmoveto 
    th setlinewidth
    0.95 setgray
    pw 0 rlineto stroke
  grestore
  % 2. Border it
  gsave
    0.7 setlinewidth
    pw 0 rlineto
    0 th neg rlineto
    pw neg 0 rlineto
    closepath stroke
  grestore
  % stk: ct rt lt
  x v get y v get th sub 1 add moveto
%%IncludeResource: font Helvetica
  fHelvetica fnfs 0.8 mul scalefont setfont
  % 3. The left title
  gsave
    dup stringwidth pop fnfs 0.8 mul add exch % leave space took on stack
    fnfs 0.8 mul hm rmoveto
    show			% left title
  grestore
  exch
  % stk: ct ltw rt
  % 4. the right title
  gsave
    dup stringwidth pop fnfs 0.8 mul add exch % leave space took on stack
    dup
    pw exch stringwidth pop fnfs 0.8 mul add sub
    hm
    rmoveto
    show			% right title
  grestore
  % stk: ct ltw rtw
  % 5. the center title
  gsave
    pw 3 1 roll
    % stk: ct pw ltw rtw
    3 copy 
    % Move to the center of the left room
    sub add 2 div hm rmoveto
    % What is the available space in here?
    add sub fnfs 0.8 mul sub fnfs 0.8 mul sub
    % stk: ct space_left
%%IncludeResource: font Helvetica-Bold
  fHelvetica-Bold fnfs scalefont setfont
    cfshow
  grestore
} bind def

% Function border: prints virtual page border
/border { %def
  gsave				% print four sides
    0 setgray
    x v get y v get moveto
    0.7 setlinewidth		% of the square
    pw 0 rlineto
    0 ph neg rlineto
    pw neg 0 rlineto
    closepath stroke
  grestore
} bind def

% Function water: prints a water mark in background
/water { %def
  gsave
    scx scy moveto rotate
%%IncludeResource: font Times-Bold
  fTimes-Bold 100 scalefont setfont
    .97 setgray
    dup stringwidth pop 2 div neg -50 rmoveto
    show
  grestore
} bind def

% Function rhead: prints the right header
/rhead {  %def
  lx ly moveto
  fHelvetica fnfs 0.8 mul scalefont setfont
  l-show
} bind def

% Function footer (cf rf lf -> -)
/footer {
  fHelvetica fnfs 0.8 mul scalefont setfont
  dx dy moveto
  show

  snx sny moveto
  l-show
  
  fnx fny moveto
  c-show
} bind def
%%EndResource
%%BeginResource: procset a2ps-black+white-Prolog 2.0 1

% Function T(ab), jumps to the n-th tabulation in the current line
/T { 
  cw mul x0 add y0 moveto
} bind def

% Function n: move to the next line
/n { %def
  /y0 y0 bfs sub store
  x0 y0 moveto
} bind def

% Function N: show and move to the next line
/N {
  Show
  /y0 y0 bfs sub store
  x0 y0 moveto
}  bind def

/S {
  Show
} bind def

/p {
  false UL
  false BX
  fCourier bfs scalefont setfont
  Show
} bind def

/sy {
  false UL
  false BX
  fSymbol bfs scalefont setfont
  Show
} bind def

/k {
  false UL
  false BX
  fCourier-Oblique bfs scalefont setfont
  Show
} bind def

/K {
  false UL
  false BX
  fCourier-Bold bfs scalefont setfont
  Show
} bind def

/c {
  false UL
  false BX
  fCourier-Oblique bfs scalefont setfont
  Show
} bind def

/C {
  false UL
  false BX
  fCourier-BoldOblique bfs scalefont setfont
  Show 
} bind def

/l {
  false UL
  false BX
  fHelvetica bfs scalefont setfont
  Show
} bind def

/L {
  false UL
  false BX
  fHelvetica-Bold bfs scalefont setfont
  Show 
} bind def

/str{
  false UL
  false BX
  fTimes-Roman bfs scalefont setfont
  Show
} bind def

/e{
  false UL
  true BX
  fHelvetica-Bold bfs scalefont setfont
  Show
} bind def

%%EndResource
%%EndProlog
%%BeginSetup
%%IncludeResource: font Courier
%%IncludeResource: font Courier-Oblique
%%IncludeResource: font Courier-Bold
%%IncludeResource: font Times-Roman
%%IncludeResource: font Symbol
%%IncludeResource: font Courier-BoldOblique
%%BeginResource: encoding ISO-8859-1Encoding
/ISO-8859-1Encoding [
/.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef 
/.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef 
/.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef 
/.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef 
/space /exclam /quotedbl /numbersign /dollar /percent /ampersand /quoteright 
/parenleft /parenright /asterisk /plus /comma /minus /period /slash 
/zero /one /two /three /four /five /six /seven 
/eight /nine /colon /semicolon /less /equal /greater /question 
/at /A /B /C /D /E /F /G 
/H /I /J /K /L /M /N /O 
/P /Q /R /S /T /U /V /W 
/X /Y /Z /bracketleft /backslash /bracketright /asciicircum /underscore 
/quoteleft /a /b /c /d /e /f /g 
/h /i /j /k /l /m /n /o 
/p /q /r /s /t /u /v /w 
/x /y /z /braceleft /bar /braceright /asciitilde /.notdef 
/.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef 
/.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef 
/.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef 
/.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef /.notdef 
/space /exclamdown /cent /sterling /currency /yen /brokenbar /section 
/dieresis /copyright /ordfeminine /guillemotleft /logicalnot /hyphen /registered /macron 
/degree /plusminus /twosuperior /threesuperior /acute /mu /paragraph /bullet 
/cedilla /onesuperior /ordmasculine /guillemotright /onequarter /onehalf /threequarters /questiondown 
/Agrave /Aacute /Acircumflex /Atilde /Adieresis /Aring /AE /Ccedilla 
/Egrave /Eacute /Ecircumflex /Edieresis /Igrave /Iacute /Icircumflex /Idieresis 
/Eth /Ntilde /Ograve /Oacute /Ocircumflex /Otilde /Odieresis /multiply 
/Oslash /Ugrave /Uacute /Ucircumflex /Udieresis /Yacute /Thorn /germandbls 
/agrave /aacute /acircumflex /atilde /adieresis /aring /ae /ccedilla 
/egrave /eacute /ecircumflex /edieresis /igrave /iacute /icircumflex /idieresis 
/eth /ntilde /ograve /oacute /ocircumflex /otilde /odieresis /divide 
/oslash /ugrave /uacute /ucircumflex /udieresis /yacute /thorn /ydieresis 
] def
%%EndResource
% Initialize page description variables.
/sh 792 def
/sw 612 def
/llx 24 def
/urx 588 def
/ury 768 def
/lly 24 def
/#copies 1 def
/th 20.000000 def
/fnfs 15 def
/bfs 10.000000 def
/cw 6.000000 def

% Dictionary for ISO-8859-1 support
/iso1dict 8 dict begin
  /fCourier ISO-8859-1Encoding /Courier reencode_font
  /fCourier-Bold ISO-8859-1Encoding /Courier-Bold reencode_font
  /fCourier-BoldOblique ISO-8859-1Encoding /Courier-BoldOblique reencode_font
  /fCourier-Oblique ISO-8859-1Encoding /Courier-Oblique reencode_font
  /fHelvetica ISO-8859-1Encoding /Helvetica reencode_font
  /fHelvetica-Bold ISO-8859-1Encoding /Helvetica-Bold reencode_font
  /fTimes-Bold ISO-8859-1Encoding /Times-Bold reencode_font
  /fTimes-Roman ISO-8859-1Encoding /Times-Roman reencode_font
currentdict end def
/bgcolor [ 0 0 0 ] def
/bg false def
/ul false def
/bx false def
% The font for line numbering
/f# /Helvetica findfont bfs .6 mul scalefont def
/fSymbol /Symbol findfont def
/hm fnfs 0.25 mul def
/pw
   cw 93.400000 mul
def
/ph
   697.000000 th add
def
/pmw 0 def
/pmh 0 def
/v 0 def
/x [
  0
] def
/y [
  pmh ph add 0 mul ph add
] def
/scx sw 2 div def
/scy sh 2 div def
/snx urx def
/sny lly 2 add def
/dx llx def
/dy sny def
/fnx scx def
/fny dy def
/lx snx def
/ly ury fnfs 0.8 mul sub def
/sx 0 def
/tab 8 def
/x0 0 def
/y0 0 def
%%EndSetup

%%Page: (1) 1
%%BeginPageSetup
/pagesave save def
%%EndPageSetup
iso1dict begin
gsave
llx lly 12 add translate
/v 0 store
/x0 x v get 4.200000 add sx cw mul add store
/y0 y v get bfs th add sub store
x0 y0 moveto
(########################################################################) c n
(#                                                                      #) N
(#       CCCCCC  SSSSSS  IIIII  RRRRRR   OOOO          L      IIIII     #) N
(#       C       S         I    R    R  O    O         L        I       #) N
(#       C       SSSSSS    I    RRRRRR  O    O  =====  L        I       #) N
(#       C            S    I    R RR    O    O         L        I       #) N
(#       CCCCCC  SSSSSS  IIIII  R   RR   OOOO          LLLLL  IIIII     #) N
(#                                                                      #) N
(########################################################################) N
(echo ") p
(   ##############################################################) str
(") p n
(echo ") S
(   #                                                            #) str
(") p n
(echo ") S
(   #  GP3xCLI                                                   #) str
(") p n
(echo ") S
(   #  GenePix Processing Program by CSIRO Livestock Industries  #) str
(") p n
(echo ") S
(   #  Bioinformatics Group                                      #) str
(") p n
(echo ") S
(   #                                                            #) str
(") p n
(echo ") S
(   #  Enquiries: Tony.Reverter-Gomez@csiro.au                   #) str
(") p n
(echo ") S
(   #  Copyright \(c\) 2003-2005 CSIRO Livestock Industries        #) str
(") p n
(echo ") S
(   #                                                            #) str
(") p n
(echo ") S
(   ##############################################################) str
(") p n
() N
(echo) N
(filename=`ls -l $1 | awk '{) S
(print) K
( $) p
(NF) K
(}'`) p n
(echo ") S
(GPR Input:) str
(" $filename | \\) p n
(   awk '{) S
(printf) K
(") p
(%3s%7s%5s%-30s\\n) str
(", $1, $2, ") p
(     ) str
(", $3}') p n
() N
(date | awk '{) S
(printf) K
(") p
(%9s%4s%5s%4s%3s%9s%4s%5s\\n) str
(", \\) p n
(             ") S
(Processed) str
(", ") p
(on:) str
(", $1, $2, $3, $4, $5, $6}') p n
(echo) N
() N
(#########################################################################) c n
(#) N
(# Column Location for bits of interest \(Starts at row 31\)) N
(#) N
(#  1. Block) S 16 T ( 2. Row) S 24 T () S 32 T ( 3. Colum ) S 48 T ( 5. Gene ID) N
(#  9. R fg Med) S 16 T (10. R fg Mean) S 32 T (12. R bg Med) S 48 T (14. R bg SD ) N
(# 18. G fg Med) S 16 T (19. G fg Mean) S 32 T (21. G bg Med) S 48 T (23. G bg SD ) N
(# 43. Q Flag) N
(#) N
(# NB: Some Gene ID contain a "." to accommodate GeneSpring limitations) N
(#     Needs to build "tempo0" file once and everything resolves from it) N
(#) N
(#########################################################################) N
() p n
(awk ') S
(NR) K
(>30 {) p
(print) K
( $5}' $1 | sed ") p
(s/\\./ /g) str
(" | awk '{) p
(print) K
( $1}' > id.nodot) p n
(awk ') S
(NR) K
(>30 {) p
(print) K
( $1, $2, $3, \\) p n
(                  $9, $10, $12, $14, \\) N
(                  $18, $19, $21, $23, \\) N
(                  $43}' $1 | \\) N
(paste - id.nodot | \\) N
(awk '{) S
(print) K
( $1, $2, $3, $13, \\) p n
(            $4, $5, $6, $7, $8, $9, $10, $11, $12}' > tempo0) N
(rm id.nodot) N
() N
(echo) N
(echo ") S
( =-=-=-=-=-=-= IMAGE QUALITY =-=-=-=-=-=-=-=) str
(") p n
(echo) N
(T=` awk '{) S
(print) K
( $0}' tempo0 | wc | awk '{) p
(print) K
( $1}'`) p n
(echo ") S
(Total No. of Spots ------------------------>) str
(" $T) p n
() N
(echo) N
(echo ") S
(  QUALITY FLAG    SPOTS) str
(") p n
(echo ") S
(  ------------    -----) str
(") p n
(awk '{) S
(print) K
( $13}' tempo0 | sort | \\) p n
(   awk ') S
(BEGIN) K
({pcg="";n=1};) p n
(        {) S
(if) K
(\($1==pcg\) n++;) p n
(         ) S
(else) K
({ ) p
(if) K
(\(pcg!=""\)) p
(printf) K
(") p
(%14s%9d\\n) str
(", pcg, n;) p n
(               n=1;) N
(               pcg=$1};) N
(        }) S
(END) K
({ ) p
(printf) K
(") p
(%14s%9d\\n) str
(", pcg, n}') p n
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() p n
(echo) N
(N=`awk '$7>$5  {) S
(print) K
( $0}' tempo0 | wc | awk '{) p
(print) K
( $1}'`) p n
(echo ") S
(Red   dye with Background >= Foreground --->) str
(" $N | \\) p n
(awk '{) S
(printf) K
(") p
(%3s%6s%5s%11s%3s%11s%5s%6d\\n) str
(", \\) p n
(             $1, $2, $3, $4, $5, $6, $7, $8}') N
() N
(N=`awk '$11>$9 {) S
(print) K
( $0}' tempo0 | wc | awk '{) p
(print) K
( $1}'`) p n
(echo ") S
(Green dye with Background >= Foreground --->) str
(" $N | \\) p n
(awk '{) S
(printf) K
(") p
(%5s%4s%5s%11s%3s%11s%5s%6d\\n) str
(", \\) p n
(             $1, $2, $3, $4, $5, $6, $7, $8}') N
() N
(echo) N
(echo ") S
( Median to Mean Correlation Analysis:) str
(") p n
(echo) N
() N
(# NB: Set zeroes to twos so their log exist) c n
() p n
(awk '$5==") S
(0) str
(" {$5=") p
(2) str
("}; $6==") p
(0) str
(" {$6=") p
(2) str
("}; \\) p n
(     $9==") S
(0) str
(" {$9=") p
(2) str
("}; $10==") p
(0) str
(" {$10=") p
(2) str
("}; \\) p n
(     {) S
(print) K
( $5, $6, $9, $10,                 \\) p n
(            ) S
(log) K
(\($5\)/) p
(log) K
(\(2\), ) p
(log) K
(\($6\)/) p
(log) K
(\(2\),   \\) p n
(            ) S
(log) K
(\($9\)/) p
(log) K
(\(2\), ) p
(log) K
(\($10\)/) p
(log) K
(\(2\)}' tempo0 > rg) p n
() N
(awk '{) S
(print) K
( \($1>$2?$2/$1:$1/$2\)}' rg > rr) p n
(awk '{) S
(print) K
( \($3>$4?$4/$3:$3/$4\)}' rg > gr) p n
(awk '{) S
(print) K
( \($5>$6?$6/$5:$5/$6\)}' rg > rl) p n
(awk '{) S
(print) K
( \($7>$8?$8/$7:$7/$8\)}' rg > gl) p n
() N
(echo ") S
(                    DATA LEFT) str
(") p n
(echo ") S
(               RED            GREEN) str
(") p n
(echo ") S
( Corr        Raw   Log2      Raw   Log2) str
(") p n
(echo ") S
( ______________________________________) str
(") p n
() N
(for) K
( minr ) p
(in) K
( 0 0.2 0.4 0.6 0.8 0.85 0.9) p n
(do) K n
(   T1=`awk -v corr=$minr '$1>corr {) p
(print) K
( $0}' rr | wc | awk '{) p
(print) K
( $1}'`) p n
(   T2=`awk -v corr=$minr '$1>corr {) S
(print) K
( $0}' rl | wc | awk '{) p
(print) K
( $1}'`) p n
(   T3=`awk -v corr=$minr '$1>corr {) S
(print) K
( $0}' gr | wc | awk '{) p
(print) K
( $1}'`) p n
(   T4=`awk -v corr=$minr '$1>corr {) S
(print) K
( $0}' gl | wc | awk '{) p
(print) K
( $1}'`) p n
(   echo ") S
(> ) str
(" $minr $T1 $T2 $T3 $T4 | \\) p n
(   awk '{) S
(printf) K
(") p
(%2s%5.2f%9d%7d%9d%7d\\n) str
(", $1, $2, $3, $4, $5, $6}') p n
(done) N
() N
(rm rg rr rl gr gl) N
() N
(echo) N
(echo ") S
( =-=-=-=-=-=-= VALID SPOTS* =-=-=-=-=-=-=-=) str
(") p n
(echo) N
(V=`awk '$13==0 && $5>$7 && $9>$11 {) S
(print) K
( $0}' tempo0 | wc | \\) p n
(   awk '{) S
(print) K
( $1}'`) p n
(echo ") S
(Total No.  of Valid Spots ----------------->) str
(" $V | \\) p n
(awk '{) S
(printf) K
(") p
(%5s%4s%4s%6s%6s%19s%6d\\n) str
(", \\) p n
(             $1, $2, $3, $4, $5, $6, $7, $8}') N
() N
(N=`echo $V $T | awk '{) S
(printf) K
(") p
(%7.1f\\n) str
(", $1/$2*100}'`) p n
(echo ") S
(Percentage of Valid Spots ----------------->) str
(" $N | \\) p n
(awk '{) S
(printf) K
(") p
(%10s%3s%6s%6s%19s%6.1f\\n) str
(", \\) p n
(             $1, $2, $3, $4, $5, $6, $7}') N
() N
(echo) N
() N
(awk '$13==0 && $5>$7 && $9>$11 {) S
(print) K
( $4}' tempo0 | sort | \\) p n
(   awk ') S
(BEGIN) K
({pcg="";n=1};              \\) p n
(        {) S
(if) K
(\($1==pcg\) n++;               \\) p n
(         ) S
(else) K
({ ) p
(if) K
(\(pcg!=""\)) p
(print) K
( pcg, n; \\) p n
(               n=1;                     \\) N
(               pcg=$1};                 \\) N
(        }) S
(END) K
({ ) p
(print) K
( pcg, n}' > gcnt) p n
(GP3xCLI.awk) (Page 2/5) (Jan 29, 06 16:37) title
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/y0 y v get bfs th add sub store
x0 y0 moveto
() p n
(G=`wc gcnt | awk '{) S
(print) K
( $1}'`) p n
(echo ") S
(Total No. of Genes ------------------------>) str
(" $G | \\) p n
(awk '{) S
(printf) K
(") p
(%5s%4s%3s%6s%26s%6d\\n) str
(", $1, $2, $3, $4, $5, $6}') p n
() N
(R=`awk '{) S
(print) K
( $2}' gcnt | awk '{sum += $1}; ) p
(END) K
({) p
(print) K
( ) p
(int) K
(\(sum/) p
(NR) K
(+0.5\)}'`) p n
(NG=`awk -v nr=$R '$2==nr {) S
(print) K
( $0}' gcnt | wc | awk '{) p
(print) K
( $1}'`) p n
(echo ") S
(Mean  No. Repetitions ----->) str
(" $R ") p
( for) str
(" $NG ") p
( Genes) str
(" | \\) p n
(   awk '{) S
(printf) K
(") p
(%4s%5s%12s%7s%4d%5s%6d%7s\\n) str
(", \\) p n
(                $1, $2, $3, $4, $5, $6, $7, $8}') N
() N
(MIN=`awk '{) S
(print) K
( $2}' gcnt | sort -n | head -1 | awk '{) p
(print) K
( $1}'`) p n
(NG=`awk -v min=$MIN '$2==min {) S
(print) K
( $0}' gcnt | wc | awk '{) p
(print) K
( $1}'`) p n
(echo ") S
(Min.  No. Repetitions ----->) str
(" $MIN ") p
( for) str
(" $NG ") p
( Genes) str
(" | \\) p n
(   awk '{) S
(printf) K
(") p
(%4s%5s%12s%7s%4d%5s%6d%7s\\n) str
(", \\) p n
(                $1, $2, $3, $4, $5, $6, $7, $8}') N
() N
(MAX=`awk '{) S
(print) K
( $2}' gcnt | sort -n | tail -1 | awk '{) p
(print) K
( $1}'`) p n
(NG=`awk -v max=$MAX '$2==max {) S
(print) K
( $0}' gcnt | wc | awk '{) p
(print) K
( $1}'`) p n
(echo ") S
(Max.  No. Repetitions ----->) str
(" $MAX ") p
( for) str
(" $NG ") p
( Genes) str
(" | \\) p n
(   awk '{) S
(printf) K
(") p
(%4s%5s%12s%7s%4d%5s%6d%7s\\n) str
(", \\) p n
(                $1, $2, $3, $4, $5, $6, $7, $8}') N
() N
(rm gcnt) N
() N
(#############################################) c n
(#  Build and process 'rgma'                 #) N
(#############################################) N
() p n
(awk '$13==0 && $5>$7 && $9>$11 {) S
(print) K
( $4, $5-$7, $9-$11}' tempo0 | \\) p n
(   awk '{) S
(print) K
( $2, $3, ) p
(log) K
(\($2/$3\)/) p
(log) K
(\(2\), 0.5*) p
(log) K
(\($2*$3\)/) p
(log) K
(\(2\)}' > rgma) p n
() N
(echo) N
(echo) N
(echo ") S
(              Log\(R/G\)  vs  0.5*Log\(R*G\)) str
(") p n
(echo ") S
(              ________      ____________) str
(") p n
() N
(awk '{) S
(print) K
( $3, $4}' rgma | \\) p n
(  awk '{ v1[) S
(NR) K
(]=$1; v2[) p
(NR) K
(]=$2}; \\) p n
(         ) S
(END) K
({ min1=min2=99999; max1=max2=-99999; \\) p n
(              ) S
(for) K
(\(i=1;i<=) p
(NR) K
(;i++\){             \\) p n
(                  ) S
(if) K
(\( v1[i] < min1 \) min1 = v1[i]; \\) p n
(                  ) S
(if) K
(\( v2[i] < min2 \) min2 = v2[i]; \\) p n
(                  ) S
(if) K
(\( v1[i] > max1 \) max1 = v1[i]; \\) p n
(                  ) S
(if) K
(\( v2[i] > max2 \) max2 = v2[i]; \\) p n
(                  s1 += v1[i]; ss1 += v1[i]*v1[i]; \\) N
(                  s2 += v2[i]; ss2 += v2[i]*v2[i]; \\) N
(                  ss12 += v1[i]*v2[i] }; \\) N
(              mean1 = s1/) S
(NR) K
(; \\) p n
(              mean2 = s2/) S
(NR) K
(; \\) p n
(              std1 = ) S
(sqrt) K
(\(\( ss1 - \(s1*s1\)/) p
(NR) K
( \) / \() p
(NR) K
(-1\)\); \\) p n
(              std2 = ) S
(sqrt) K
(\(\( ss2 - \(s2*s2\)/) p
(NR) K
( \) / \() p
(NR) K
(-1\)\); \\) p n
(              num = \( ss12 - \(s1*s2\)/) S
(NR) K
( \) / \() p
(NR) K
(-1\); \\) p n
(              den = std1 * std2; \\) N
(              corr = num / den; \\) N
(     ) S
(printf) K
(") p
(%10s%11d%17d\\n) str
(",") p
(N) str
(",) p
(NR) K
(,) p
(NR) K
(; \\) p n
(     ) S
(printf) K
(") p
(%10s%11.3f%17.3f\\n) str
(",") p
(Mean) str
(",mean1,mean2; \\) p n
(     ) S
(printf) K
(") p
(%10s%11.3f%17.3f\\n) str
(",") p
(Std) str
(",std1,std2; \\) p n
(     ) S
(printf) K
(") p
(%10s%11.3f%17.3f\\n) str
(",") p
(Min) str
(",min1,min2; \\) p n
(     ) S
(printf) K
(") p
(%10s%11.3f%17.3f\\n) str
(",") p
(Max) str
(",max1,max2; \\) p n
(     ) S
(printf) K
(") p
(%18s%10.3f\\n) str
(",") p
(Correlation) str
(",corr; \\) p n
(     }') N
() N
() N
(echo) N
(echo ") S
(       Log\(R/G\) across Intensity Values ) str
(") p n
(echo ") S
(      Intensity     Spots    % <0   % >0) str
(") p n
(echo ") S
(      __________________________________) str
(") p n
() N
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x0 y0 moveto
(LOW=0) p n
(UPP=4) N
(MAX=16) N
(while) K
( [ $UPP -le $MAX ]) p n
(do) K n
() p n
(   T=`awk -v min=$LOW -v max=$UPP \\) N
(      '$4>=min && $4<max {) S
(print) K
( $4}'  rgma | wc -l`) p n
(   P=`awk -v min=$LOW -v max=$UPP \\) N
(      '$4>=min && $4<max && $3>0 {) S
(print) K
( $4}' rgma | wc -l`) p n
(   N=`awk -v min=$LOW -v max=$UPP \\) N
(      '$4>=min && $4<max && $3<=0 {) S
(print) K
( $4}' rgma | wc -l`) p n
() N
(   P=`echo $P $T | awk '$2>0 {$3=$1/$2*100}; $2==0 {$3=0}; {) S
(print) K
( $3}'`) p n
(   N=`echo $N $T | awk '$2>0 {$3=$1/$2*100}; $2==0 {$3=0}; {) S
(print) K
( $3}'`) p n
(   echo ") S
(\() str
(" $LOW ") p
(,) str
(" $UPP ") p
(\)  ) str
(" $T $N $P | \\) p n
(   awk '{) S
(printf) K
(") p
(%7s%2d%2s%3d%-2s%9d%8.1f%7.1f\\n) str
(", \\) p n
(                $1, $2, $3, $4, $5, $6, $7, $8}') N
() N
(   LOW=`expr $LOW + 4`) N
(   UPP=`expr $UPP + 4`) N
(done) N
(echo ") S
(      __________________________________) str
(") p n
() N
(echo) N
(echo ") S
(*NB: Valid Spot defined as spots with Background < Foreground for) str
(") p n
(echo ") S
(     both Red and Green channels and with a Quality Flag of 0.) str
(") p n
() N
(#############################################) c n
(# Compute densities of variables in rgma file) N
(#############################################) N
() p n
(awk '{) S
(print) K
( ) p
(log) K
(\($1\)/) p
(log) K
(\(2\)}' rgma | sort -n | \\) p n
(   awk '{ data[) S
(NR) K
(] = $1 };) p n
(        ) S
(END) K
( { min = data[1]; max = data[) p
(NR) K
(]; range = max - min;) p n
(              n_int = \( ) S
(int) K
(\() p
(NR) K
(/10\) > 1000 ? 1000: ) p
(int) K
(\() p
(NR) K
(/10\) \)) p n
(              size = range / n_int;) N
(              mn_int = min + size/2;) N
(              ) S
(for) K
(\(i=1; i<=) p
(NR) K
(; i++\){) p n
(                    aux = ) S
(int) K
(\(\(data[i] - min\)/size\) + 1;) p n
(                    q[aux]++;) N
(              };) N
(              ) S
(for) K
(\(i=1; i<=n_int; i++\){) p n
(                    ) S
(if) K
(\( q[i] < 1 \) q[i] = 1;) p n
(                    ) S
(print) K
( mn_int, q[i];) p n
(                    mn_int += size;) N
(              };) N
(        }' > logr.d) N
() N
(awk '{) S
(print) K
( ) p
(log) K
(\($2\)/) p
(log) K
(\(2\)}' rgma | sort -n | \\) p n
(   awk '{ data[) S
(NR) K
(] = $1 };) p n
(        ) S
(END) K
( { min = data[1]; max = data[) p
(NR) K
(]; range = max - min;) p n
(              n_int = \( ) S
(int) K
(\() p
(NR) K
(/10\) > 1000 ? 1000: ) p
(int) K
(\() p
(NR) K
(/10\) \)) p n
(              size = range / n_int;) N
(              mn_int = min + size/2;) N
(              ) S
(for) K
(\(i=1; i<=) p
(NR) K
(; i++\){) p n
(                    aux = ) S
(int) K
(\(\(data[i] - min\)/size\) + 1;) p n
(                    q[aux]++;) N
(              };) N
(              ) S
(for) K
(\(i=1; i<=n_int; i++\){) p n
(                    ) S
(if) K
(\( q[i] < 1 \) q[i] = 1;) p n
(                    ) S
(print) K
( mn_int, q[i];) p n
(                    mn_int += size;) N
(              };) N
(        }' > logg.d) N
() N
(awk '{) S
(printf) K
(") p
(%10.5f\\n) str
(", $3}' rgma | sort -n | \\) p n
(   awk '{ data[) S
(NR) K
(] = $1 };) p n
(        ) S
(END) K
( { min = data[1]; max = data[) p
(NR) K
(]; range = max - min;) p n
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iso1dict begin
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/v 0 store
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/y0 y v get bfs th add sub store
x0 y0 moveto
(              n_int = \( ) p
(int) K
(\() p
(NR) K
(/10\) > 1000 ? 1000: ) p
(int) K
(\() p
(NR) K
(/10\) \)) p n
(              size = range / n_int;) N
(              mn_int = min + size/2;) N
(              ) S
(for) K
(\(i=1; i<=) p
(NR) K
(; i++\){) p n
(                    aux = ) S
(int) K
(\(\(data[i] - min\)/size\) + 1;) p n
(                    q[aux]++;) N
(              };) N
(              ) S
(for) K
(\(i=1; i<=n_int; i++\){) p n
(                    ) S
(if) K
(\( q[i] < 1 \) q[i] = 1;) p n
(                    ) S
(print) K
( mn_int, q[i];) p n
(                    mn_int += size;) N
(              };) N
(        }' > m.d) N
() N
(awk '{) S
(print) K
( $4}' rgma | sort -n | \\) p n
(   awk '{ data[) S
(NR) K
(] = $1 };) p n
(        ) S
(END) K
( { min = data[1]; max = data[) p
(NR) K
(]; range = max - min;) p n
(              n_int = \( ) S
(int) K
(\() p
(NR) K
(/10\) > 1000 ? 1000: ) p
(int) K
(\() p
(NR) K
(/10\) \)) p n
(              size = range / n_int;) N
(              mn_int = min + size/2;) N
(              ) S
(for) K
(\(i=1; i<=) p
(NR) K
(; i++\){) p n
(                    aux = ) S
(int) K
(\(\(data[i] - min\)/size\) + 1;) p n
(                    q[aux]++;) N
(              };) N
(              ) S
(for) K
(\(i=1; i<=n_int; i++\){) p n
(                    ) S
(if) K
(\( q[i] < 1 \) q[i] = 1;) p n
(                    ) S
(print) K
( mn_int, q[i];) p n
(                    mn_int += size;) N
(              };) N
(        }' > a.d) N
() N
(rm tempo0) N
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%%EOF