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Full Discussion: [Solved] File reformat
Top Forums Shell Programming and Scripting [Solved] File reformat Post 302886523 by cmccabe on Saturday 1st of February 2014 10:21:47 AM
Old 02-01-2014
[Solved] File reformat
I am using the code below to reformat the input (hp.txt). The output (newhp.txt) is not in the desired format and I can not seem to figure it out. I have attached both. Thank you.

Code:
 perl -aF/\\t/ -lne 'print join(" ",@F[0,1,2,$_,5]) for ("0 A","0 G","0 C","0 T","A 0","G 0","C 0","T 0")' hp.txt > newhp.txt

So in hp.txt the file looks like:
Code:
2    39224622    3922462       -       T         intron_7homopolymer
3    12632440    12632440     -        C        CDS_4homopolymer

Desired Output of newhp.txt
Code:
2  39224622  39224622   0   A  intron_7homopolymer 
2  39224622  39224622   0   T intron_7homopolymer
2  39224622  39224622   0   C intron_7homopolymer
2  39224622  39224622   0   G intron_7homopolymer
2  39224622  39224622   A   0 intron_7homopolymer
2  39224622  39224622   T   0 intron_7homopolymer
2  39224622  39224622   C   0 intron_7homopolymer
2  39224622  39224622   G   0 intron_7homopolymer
3  12632440  12632440   0   A CDS_4homopolymer
3  12632440  12632440   0   T CDS_4homopolymer
3  12632440  12632440   0   C CDS_4homopolymer
3  12632440  12632440   0   G CDS_4homopolymer
3  12632440  12632440   A   0 CDS_4homopolymer
3  12632440  12632440   T   0 CDS_4homopolymer
3  12632440  12632440   C   0 CDS_4homopolymer
3  12632440  12632440   G   0 CDS_4homopolymer

hp.txt (61.2 KB) 
newhp.txt (475.4 KB) 
Last edited by bartus11; 02-01-2014 at 11:30 AM.. Reason: Please use [code][/code] tags for input and output data.
 

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LEARN ABOUT REDHAT

unix2dos

unix2dos(1)						      General Commands Manual						       unix2dos(1)

NAME

       unix2dos - UNIX to DOS text file format converter

SYNOPSYS

       unix2dos [options] [-c convmode] [-o file ...] [-n infile outfile ...]

       Options:

       [-hkqV] [--help] [--keepdate] [--quiet] [--version]

DESCRIPTION

       This manual page documents unix2dos, the program that converts text files in UNIX format to DOS format.

OPTIONS

       The following options are available:

       -h --help
	      Print online help.

       -k --keepdate
	      Keep the date stamp of output file same as input file.

       -q --quiet
	      Quiet mode. Suppress all warning and messages.

       -V --version
	      Prints version information.

       -c --convmode convmode
	      Sets conversion mode. Simulates unix2dos under SunOS.

       -o --oldfile file ...
	      Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used.

       -n --newfile infile outfile ...
	      New  file  mode.	Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be
	      used or you WILL lost your files.

EXAMPLES

       Get input from stdin and write output to stdout.

	      unix2dos

       Convert and replace a.txt. Convert and replace b.txt.

	      unix2dos a.txt b.txt

	      unix2dos -o a.txt b.txt

       Convert and replace a.txt in ASCII conversion mode.  Convert and replace b.txt in ISO conversion mode.

	      unix2dos a.txt -c iso b.txt

	      unix2dos -c ascii a.txt -c iso b.txt

       Convert and replace a.txt while keeping original date stamp.

	      unix2dos -k a.txt

	      unix2dos -k -o a.txt

       Convert a.txt and write to e.txt.

	      unix2dos -n a.txt e.txt

       Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt.

	      unix2dos -k -n a.txt e.txt

       Convert and replace a.txt. Convert b.txt and write to e.txt.

	      unix2dos a.txt -n b.txt e.txt

	      unix2dos -o a.txt -n b.txt e.txt

       Convert c.txt and write to e.txt. Convert and replace a.txt.  Convert and replace b.txt. Convert d.txt and write to f.txt.

	      unix2dos -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt

DIAGNOSTICS

BUGS

       The program does not work properly under MSDOS in stdio processing mode.  If you know why is that so, please tell me.

AUTHOR

       Benjamin Lin - ( blin@socs.uts.edu.au )

MISCELLANY

       Tested environment:

	      Linux 1.2.0 with GNU C 2.5.8

	      SunOS 4.1.3 with GNU C 2.6.3

	      MS-DOS 6.20 with Borland C++ 4.02

       Suggestions and bug reports are welcome.

SEE ALSO

       dos2unix(1)

1995.03.31							   unix2dos v2.2						       unix2dos(1)
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