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Full Discussion: Change directory shell
Top Forums Shell Programming and Scripting Change directory shell Post 302922805 by cmccabe on Tuesday 28th of October 2014 11:28:20 AM
Old 10-28-2014
Code:
 #!/bin/bash
echo -n "Enter number of sanger patients  : "; read id
cd 'C:\Users\cmccabe\Desktop\annovar'
perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt

Code:
  bash ~/sanger.sh
Enter number of sanger patients  : 2
': not a valid identifierline 2: read: `id
: No such file or directoryne 3: cd: C:\Users\cmccabe\Desktop\annovar
/home/cmccabe/sanger.sh: line 4: file.txt: No such file or directory

Maybe:
Code:
 while true
do
        printf "Enter ID  : " ; read id
        [ -z "$id" ] && break
        cd 'C:\Users\cmccabe\Desktop\annovar'
        perl -ne 'chomp; system ("perl table_annovar.pl $_ humandb/ -buildver hg19 -protocol refGene,popfreq_all,common,clinvar,clinvarsubmit,clinvarreference -operation g,f,f,f,f,f -otherinfo")' < file.txt
done

Thanks Smilie.
Last edited by cmccabe; 10-28-2014 at 12:34 PM..
 

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LEARN ABOUT DEBIAN

sdl::gfx::imagefilter

pods::SDL::GFX::ImageFilter(3pm)			User Contributed Perl Documentation			  pods::SDL::GFX::ImageFilter(3pm)

NAME

       SDL::GFX::ImageFilter - image filtering functions

CATEGORY

       TODO, GFX

METHODS

   MMX_detect
       int gfx_image_MMX_detect()      CODE:	       SDL_imageFilterMMXdetect();

   MMX_off
       void gfx_image_MMX_off()      CODE:	     SDL_imageFilterMMXoff();

   MMX_on
       void gfx_image_MMX_on()	    CODE:	    SDL_imageFilterMMXon();

   add
       int gfx_image_add(Src1, Src2, Dest, length)	unsigned char *Src1	 unsigned char *Src2	  unsigned char *Dest	   int length
	    CODE:	    RETVAL = SDL_imageFilterAdd(Src1, Src2, Dest, length);	OUTPUT: 	  RETVAL

   mean
       int gfx_image_mean(Src1, Src2, Dest, length)	 unsigned char *Src1	  unsigned char *Src2	   unsigned char *Dest	    int length
	    CODE:	    RETVAL = SDL_imageFilterMean(Src1, Src2, Dest, length);	 OUTPUT:	   RETVAL

   sub
       int gfx_image_sub(Src1, Src2, Dest, length)	unsigned char *Src1	 unsigned char *Src2	  unsigned char *Dest	   int length
	    CODE:	    RETVAL = SDL_imageFilterSub(Src1, Src2, Dest, length);	OUTPUT: 	  RETVAL

   abs_diff
       int gfx_image_abs_diff(Src1, Src2, Dest, length)      unsigned char *Src1      unsigned char *Src2      unsigned char *Dest	int length
	    CODE:	    RETVAL = SDL_imageFilterAbsDiff(Src1, Src2, Dest, length);	    OUTPUT:	      RETVAL

   mult
       int gfx_image_mult(Src1, Src2, Dest, length)	 unsigned char *Src1	  unsigned char *Src2	   unsigned char *Dest	    int length
	    CODE:	    RETVAL = SDL_imageFilterMult(Src1, Src2, Dest, length);	 OUTPUT:	   RETVAL

   mult_nor
       int gfx_image_mult_nor(Src1, Src2, Dest, length)      unsigned char *Src1      unsigned char *Src2      unsigned char *Dest	int length
	    CODE:	    RETVAL = SDL_imageFilterMultNor(Src1, Src2, Dest, length);	    OUTPUT:	      RETVAL

   mult_div_by_2
       int gfx_image_mult_div_by_2(Src1, Src2, Dest, length)	  unsigned char *Src1	   unsigned char *Src2	    unsigned char *Dest      int
       length	   CODE:	   RETVAL = SDL_imageFilterMultDivby2(Src1, Src2, Dest, length);      OUTPUT:		RETVAL

   mult_div_by_4
       int gfx_image_mult_div_by_4(Src1, Src2, Dest, length)	  unsigned char *Src1	   unsigned char *Src2	    unsigned char *Dest      int
       length	   CODE:	   RETVAL = SDL_imageFilterMultDivby4(Src1, Src2, Dest, length);      OUTPUT:		RETVAL

   bit_and
       int gfx_image_bit_and(Src1, Src2, Dest, length)	    unsigned char *Src1      unsigned char *Src2      unsigned char *Dest      int length
	    CODE:	    RETVAL = SDL_imageFilterBitAnd(Src1, Src2, Dest, length);	   OUTPUT:	     RETVAL

   bit_or
       int gfx_image_bit_or(Src1, Src2, Dest, length)	   unsigned char *Src1	    unsigned char *Src2      unsigned char *Dest      int length
	    CODE:	    RETVAL = SDL_imageFilterBitOr(Src1, Src2, Dest, length);	  OUTPUT:	    RETVAL

   div
       int gfx_image_div(Src1, Src2, Dest, length)	unsigned char *Src1	 unsigned char *Src2	  unsigned char *Dest	   int length
	    CODE:	    RETVAL = SDL_imageFilterDiv(Src1, Src2, Dest, length);	OUTPUT: 	  RETVAL

   bit_negation
       int gfx_image_bit_negation(Src1, Dest, length)	   unsigned char *Src1	    unsigned char *Dest      int length      CODE:
		 RETVAL = SDL_imageFilterBitNegation(Src1, Dest, length);      OUTPUT:		 RETVAL

   add_byte
       int gfx_image_add_byte(Src1, Dest, length, C)	  unsigned char *Src1	   unsigned char *Dest	    int length	    unsigned char C
	    CODE:	    RETVAL = SDL_imageFilterAddByte(Src1, Dest, length, C);	 OUTPUT:	   RETVAL

   add_uint
       int gfx_image_add_uint(Src1, Dest, length, C)	  unsigned char *Src1	   unsigned char *Dest	    int length	    unsigned int C
	    CODE:	    RETVAL = SDL_imageFilterAddUint(Src1, Dest, length, C);	 OUTPUT:	   RETVAL

   add_byte_to_half
       int gfx_image_add_byte_to_half(Src1, Dest, length, C)	  unsigned char *Src1	   unsigned char *Dest	    int length	    unsigned char
       C      CODE:	      RETVAL = SDL_imageFilterAddByteToHalf(Src1, Dest, length, C);	 OUTPUT:	   RETVAL

   sub_byte
       int gfx_image_sub_byte(Src1, Dest, length, C)	  unsigned char *Src1	   unsigned char *Dest	    int length	    unsigned char C
	    CODE:	    RETVAL = SDL_imageFilterSubByte(Src1, Dest, length, C);	 OUTPUT:	   RETVAL

   sub_uint
       int gfx_image_sub_uint(Src1, Dest, length, C)	  unsigned char *Src1	   unsigned char *Dest	    int length	    unsigned int C
	    CODE:	    RETVAL = SDL_imageFilterSubUint(Src1, Dest, length, C);	 OUTPUT:	   RETVAL

   shift_right
       int gfx_image_shift_right(Src1, Dest, length, N)      unsigned char *Src1      unsigned char *Dest      int length      unsigned char N
	    CODE:	    RETVAL = SDL_imageFilterShiftRight(Src1, Dest, length, N);	    OUTPUT:	      RETVAL

   shift_right_uint
       int gfx_image_shift_right_uint(Src1, Dest, length, N)	  unsigned char *Src1	   unsigned char *Dest	    int length	    unsigned char
       N      CODE:	      RETVAL = SDL_imageFilterShiftRightUint(Src1, Dest, length, N);	  OUTPUT:	    RETVAL

   mult_by_byte
       int gfx_image_mult_by_byte(Src1, Dest, length, C)      unsigned char *Src1      unsigned char *Dest	int length	unsigned char C
	    CODE:	    RETVAL = SDL_imageFilterMultByByte(Src1, Dest, length, C);	    OUTPUT:	      RETVAL

   shift_right_and_mult_by_byte
       int gfx_image_shift_right_and_mult_by_byte(Src1, Dest, length, N, C)	 unsigned char *Src1	  unsigned char *Dest	   int length
	    unsigned char N	 unsigned char C      CODE:	      RETVAL = SDL_imageFilterShiftRightAndMultByByte(Src1, Dest, length, N, C);
	    OUTPUT:	      RETVAL

   shift_left_byte
       int gfx_image_shift_left_byte(Src1, Dest, length, N)	 unsigned char *Src1	  unsigned char *Dest	   int length	   unsigned char N
	    CODE:	    RETVAL = SDL_imageFilterShiftLeftByte(Src1, Dest, length, N);      OUTPUT:		 RETVAL

   shift_left_uint
       int gfx_image_shift_left_uint(Src1, Dest, length, N)	 unsigned char *Src1	  unsigned char *Dest	   int length	   unsigned char N
	    CODE:	    RETVAL = SDL_imageFilterShiftLeftUint(Src1, Dest, length, N);      OUTPUT:		 RETVAL

   shift_left
       int gfx_image_shift_left(Src1, Dest, length, N)	    unsigned char *Src1      unsigned char *Dest      int length      unsigned char N
	    CODE:	    RETVAL = SDL_imageFilterShiftLeft(Src1, Dest, length, N);	   OUTPUT:	     RETVAL

   binarize_using_threshold
       int gfx_image_binarize_using_threshold(Src1, Dest, length, T)	  unsigned char *Src1	   unsigned char *Dest	    int length
	    unsigned char T	 CODE:		 RETVAL = SDL_imageFilterBinarizeUsingThreshold(Src1, Dest, length, T);      OUTPUT:
		 RETVAL

   clip_to_range
       int gfx_image_clip_to_range(Src1, Dest, length, Tmin, Tmax)	unsigned char *Src1	 unsigned char *Dest	  int length	  unsigned
       char Tmin      unsigned char Tmax      CODE:	      RETVAL = SDL_imageFilterClipToRange(Src1, Dest, length, Tmin, Tmax);	OUTPUT:
		 RETVAL

   normalize_linear
       int gfx_image_normalize_linear(Src1, Dest, length, Cmin, Cmax, Nmin, Nmax)      unsigned char *Src1	unsigned char *Dest	 int
       length	   int Cmin	 int Cmax      int Nmin      int Nmax	   CODE:	   RETVAL = SDL_imageFilterNormalizeLinear(Src1, Dest,
       length, Cmin, Cmax, Nmin, Nmax);      OUTPUT:	       RETVAL

   convolve_kernel_3x3_divide
       int gfx_image_convolve_kernel_3x3_divide(Src, Dest, rows, columns, Kernel, Divisor)	unsigned char *Src	unsigned char *Dest
	    int rows	  int columns	   Sint16 *Kernel      unsigned char Divisor	  CODE: 	  RETVAL =
       SDL_imageFilterConvolveKernel3x3Divide(Src, Dest, rows, columns, Kernel, Divisor);      OUTPUT:		 RETVAL

   convolve_kernel_5x5_divide
       int gfx_image_convolve_kernel_5x5_divide(Src, Dest, rows, columns, Kernel, Divisor)	unsigned char *Src	unsigned char *Dest
	    int rows	  int columns	   Sint16 *Kernel      unsigned char Divisor	  CODE: 	  RETVAL =
       SDL_imageFilterConvolveKernel5x5Divide(Src, Dest, rows, columns, Kernel, Divisor);      OUTPUT:		 RETVAL

   convolve_kernel_7x7_divide
       int gfx_image_convolve_kernel_7x7_divide(Src, Dest, rows, columns, Kernel, Divisor)	unsigned char *Src	unsigned char *Dest
	    int rows	  int columns	   Sint16 *Kernel      unsigned char Divisor	  CODE: 	  RETVAL =
       SDL_imageFilterConvolveKernel7x7Divide(Src, Dest, rows, columns, Kernel, Divisor);      OUTPUT:		 RETVAL

   convolve_kernel_9x9_divide
       int gfx_image_convolve_kernel_9x9_divide(Src, Dest, rows, columns, Kernel, Divisor)	unsigned char *Src	unsigned char *Dest
	    int rows	  int columns	   Sint16 *Kernel      unsigned char Divisor	  CODE: 	  RETVAL =
       SDL_imageFilterConvolveKernel9x9Divide(Src, Dest, rows, columns, Kernel, Divisor);      OUTPUT:		 RETVAL

   convolve_kernel_3x3_shift_right
       int gfx_image_convolve_kernel_3x3_shift_right(Src, Dest, rows, columns, Kernel, NRightShift)	 unsigned char *Src	 unsigned char
       *Dest	  int rows	int columns	 Sint16 *Kernel      unsigned char NRightShift	    CODE:	    RETVAL =
       SDL_imageFilterConvolveKernel3x3ShiftRight(Src, Dest, rows, columns, Kernel, NRightShift);      OUTPUT:		 RETVAL

   convolve_kernel_5x5_shift_right
       int gfx_image_convolve_kernel_5x5_shift_right(Src, Dest, rows, columns, Kernel, NRightShift)	 unsigned char *Src	 unsigned char
       *Dest	  int rows	int columns	 Sint16 *Kernel      unsigned char NRightShift	    CODE:	    RETVAL =
       SDL_imageFilterConvolveKernel5x5ShiftRight(Src, Dest, rows, columns, Kernel, NRightShift);      OUTPUT:		 RETVAL

   convolve_kernel_7x7_shift_right
       int gfx_image_convolve_kernel_7x7_shift_right(Src, Dest, rows, columns, Kernel, NRightShift)	 unsigned char *Src	 unsigned char
       *Dest	  int rows	int columns	 Sint16 *Kernel      unsigned char NRightShift	    CODE:	    RETVAL =
       SDL_imageFilterConvolveKernel7x7ShiftRight(Src, Dest, rows, columns, Kernel, NRightShift);      OUTPUT:		 RETVAL

   convolve_kernel_9x9_shift_right
       int gfx_image_convolve_kernel_9x9_shift_right(Src, Dest, rows, columns, Kernel, NRightShift)	 unsigned char *Src	 unsigned char
       *Dest	  int rows	int columns	 Sint16 *Kernel      unsigned char NRightShift	    CODE:	    RETVAL =
       SDL_imageFilterConvolveKernel9x9ShiftRight(Src, Dest, rows, columns, Kernel, NRightShift);      OUTPUT:		 RETVAL

   sobel_x
       int gfx_image_sobel_x(Src, Dest, rows, columns)	    unsigned char *Src	    unsigned char *Dest      int rows	   int columns	    CODE:
		 RETVAL = SDL_imageFilterSobelX(Src, Dest, rows, columns);	OUTPUT: 	  RETVAL

   sobel_x_shift_right
       int gfx_image_sobel_x_shift_right(Src, Dest, rows, columns, NRightShift)      unsigned char *Src      unsigned char *Dest      int rows
	    int columns      unsigned char NRightShift	    CODE:	    RETVAL = SDL_imageFilterSobelXShiftRight(Src, Dest, rows, columns,
       NRightShift);	  OUTPUT:	    RETVAL

   align_stack
       void gfx_image_align_stack()	 CODE:		 SDL_imageFilterAlignStack();

   restore_stack
       void gfx_image_restore_stack()	   CODE:	   SDL_imageFilterRestoreStack();

AUTHORS

       See "AUTHORS" in SDL.

perl v5.14.2							    2012-05-28					  pods::SDL::GFX::ImageFilter(3pm)
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