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Top Forums Shell Programming and Scripting Help with calculating frequency of specific word in a string Post 302578917 by perl_beginner on Saturday 3rd of December 2011 01:38:07 AM
Old 12-03-2011
Help with calculating frequency of specific word in a string

Input file:
Code:
#read_1
AWEAWQQRZZZQWQQWZ
#read_2
ZZAQWRQTWQQQWADSADZZZ
#read_3
POGZZZZZZADWRR
.
.

Desired output file:
Code:
#read_1 3
#read_1 1
#read_2 2
#read_2 3
#read_3 6
.
.

Perl script that I have tried:
Code:
#!/usr/bin/perl 

$/ = ">";


while (<>) {
	next if $. ==  1;
	chomp;

	my($header,@other) =  split(/\n/,$_);
	$sequence = join"",@other;

	my @letters = split"",$sequence;
	$seqlength = length $sequence;
	$counter = 0;

	foreach $base (@letters) {
		$counter++ if $base eq 'Z';
	}
	print ">$header\t$counter\n";	
	
}

Command I have tried:
Code:
[home@user]perl count.pl input_file.txt > input_file.stats
[home@user]cat input_file.stats
#read_1 4
#read_2 5
#read_3 6
.
.

My purpose is to calculate the frequency of "Z" at each string in detail.
However, I only able to total sum all the frequency of "Z" in each string.

Thanks for any advice.
 

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fb.modes(5)						     Linux frame buffer utils						       fb.modes(5)

NAME
fb.modes - frame buffer modes file DESCRIPTION
/etc/fb.modes contains an unlimited number of video mode descriptions. The general format of a video mode is: mode geometry <xres> <yres> <vxres> <vyres> <depth> timings <pixclock> <left> <right> <upper> <lower> <hslen> <vslen> options <value> rgba <red,green,blue,alpha> endmode OPTIONS
geometry options: xres visible horizontal resolution (in pixels) yres visible vertical resolution (in pixels) vxres virtual horizontal resolution (in pixels) vyres virtual vertical resolution (in pixels) depth display depth (in bits per pixel) timing options: pixclock length of one pixel (in picoseconds) left left margin (in pixels) right right margin (in pixels) upper upper margin (in pixel lines) lower lower margin (in pixel lines) hslen horizontal sync length (in pixels) vslen vertical sync length (in pixel lines) rgba options (only valid with truecolor): red red color bitfields (in length or length/offset) green green color bitfields (in length or length/offset) blue blue color bitfields (in length or length/offset) alpha alpha color bitfields (in length or length/offset) other options: the first value of this options is the default hsync {low|high} the horizontal sync polarity vsync {low|high} the vertical sync polarity csync {low|high} the composite sync polarity gsync {low|high} the sync on green polarity bcast {false|true} enable or disable broadcast modes. If enabled the frame buffer generates the exact timings fot several broadcast modes (e.g. PAL or NTSC). Note that this option may not be supported by every frame buffer extsync {false|true} enable or disable external resync. If enabled the sync timings are not generated by the frame buffer device and must be pro- vided externally instead. Note that this option may not be supported by every frame buffer device laced {false|true} enable or disable interlace. If enabled the display will be split in two frames, each frame contains only even and odd lines respectively. These two frames will be displayed alternating, this way twice the lines can be displayed and the vertical fre- quency for monitor stays the same, but the visible vertical frequency gets halved double {false|true} enable or disable doublescan. If enabled every line will be displayed twice and this way the horizontal frequency can easily be doubled, so that the same resolution can be displayed on different monitors, even if the horizontal frequency specifica- tion differs. Note that this option may not be supported by every frame buffer device nostd <number> select nonstandard video mode accel {false|true} enable or disable hardware text acceleration grayscale {false|true} enable or disable graylevels instead of colors INTERNALS
Generally a frame buffer display is organized as follows: +---+---------------+---+---+ | | ^ | | | | | | 5 | | | | | v | | | +---#################---+---+ | # ^ # | | | # | # | | | # | # | | | 1 # | 2 # 3 | 4 | |<->#<------+------>#<->|<->| | # | # | | | # | 6 # | | | # | # | | | # v # | | +---#################---+---+ | | ^ | | | | | | 7 | | | | | v | | | +---+---------------+---+---+ | | ^ | | | | | | 8 | | | | | v | | | +---+---------------+---+---+ 1 left margin 2 xres 3 right margin 4 horizontal sync len 5 upper margin 6 yres 7 lower margin 8 vertical sync len The area bordered with `#' is the visible display area. Horizontal and vertical frequencies can now easily be calculated, for this the sum of horizontal or vertical values are important htotal = left + xres + right + hslen vtotal = upper + yres + lower + vslen The length of one line can now be calculated with pixclock line = pixclock * htotal and we have the horizontal frequency hfreq = 1E12 / line = 1E12 / (pixclock * htotal) To get the vertical frequency vtotal must eventually adjusted. If the display is laced, vtotal must be halved or if the display is a dou- blescan one, vtotal must be doubled. Now we can calculate the length of one frame if (lace) vtotal /= 2 if (double) vtotal *= 2 frame = vtotal * line and we get also the vertical frequency vfreq = 1E12 / frame = hfreq / vtotal SEE ALSO
fbset(8), fbdev(4) 2.1 2003-08-07 fb.modes(5)
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