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Full Discussion: Modifications to a file
Top Forums Shell Programming and Scripting Modifications to a file Post 302370498 by kylle345 on Wednesday 11th of November 2009 03:57:25 PM
Old 11-11-2009
Modifications to a file

Hi,

I do not have a clue how to do this nor can I find information on it but I have a file that looks like this (basically 3 columns and tab delimited). I need this in a particular format in order for a program to actually read it.

Code:
chr1  2  4
chr1  2  5
chr1  3  6
chr2  1  4
chr2  2  5

what I want to do is this

Code:
track type=wiggle_0 name="Name" description="Name" visibility=full autoScale=off viewLimits=-5:1.25 color=0,100,0 altColor=0,100,0 priority=30 yLineOnOff=on 
variableStep chrom=chr1 span=1
2  4
2  5
3  6

track type=wiggle_0 name="Name" description="Name" visibility=full autoScale=off viewLimits=-5:1.25 color=0,100,0 altColor=0,100,0 priority=30 yLineOnOff=on 
variableStep chrom=chr2 span=1
1  4
2  5

so basically when an identifier changes along chr1 then a header (above) is added containing the track type etc... (the header is space separeted) and then at chrom = , a name from column 1 is added (chr1 etc....). Am I clear here?

thanks
 

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YAGI(5) 							File Formats Manual							   YAGI(5)

NAME
yagi - yagi binary output format DESCRIPTION
This manual page describes the output format of the file created by the Yagi-Uda project's yagi program. The file is a binary file with a header of 100 bytes. The header consists of: offset(bytes) information data-type 0 elements int 4 driven int 8 parasitic int 12 min_frequency double 20 max_frequency double 28 design frequency double 36 step_frequency double 44 angular_step double 52 0 double 92 0 double Following the header, there starts the coordinates(x,y,l) of each element and the voltage applied to each element. Then we write the element currents one after the other, at each frequency. Hence the element currents will be written 12,000 times with a 3 element yagi analysed at 4,000 different frequencies. All complex data is stored in a structure of type fcomplex, defined as: struct fcomplex {double real, double imaginary}; offset(bytes) information data-type 100 x1 double /* coordinates */ 108 y1 double 116 l1 double 100+(n-1)*24 x_n double 100+(n-1)*24+8 y_n double 100+(n-1)*24+16 l_n double -------------- Repeated for each element. 100+24*elements Voltage1 fcomplex /* voltage */ 100+24*elements+(n-1)*16 Voltage_n fcomplex -------------- Repeated for each element n at each frequency step f. 100+40*elements Current1@f1 fcomplex /* current */ 100+40*elements+(n-1)*16 Current_n@f1 fcomplex 100+56*elements Current@f2 fcomplex 100+40*elements+(n-1)*16 Current_n@f2 fcomplex FILES
filename.out binary file SEE ALSO
yagi(1), output(1), input(1), optimise(1), first(1) and input(5). AUTHORS
Dr. David Kirkby G8WRB (david.kirkby@onetel.net), with help with converting to DOS from Dr. Joe Mack NA3T (mack@fcrfv2.ncifcrf.gov). Yagi version 1.16 24th October 2000 YAGI(5)
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