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Full Discussion: Make multiple awk files into an executable
Top Forums Shell Programming and Scripting Make multiple awk files into an executable Post 302604670 by jacobs.smith on Monday 5th of March 2012 03:37:44 PM
Old 03-05-2012
Make multiple awk files into an executable
Hello everyone,

The following are my input files.

Quote:
1.txt
chr1 14765298 14766727 def
chr1 16759093 16760238 def
chr1 16759236 16760238 def
chr1 20782516 20784428 him
chr1 20989962 20991078 her
chr2 31672150 31673532 abc
chr2 33157721 33158124 abc
chr3 34542283 34542962 abc
chr3 38248682 38251416 abc
chr4 58562053 58567653 abc
............................................
............................................
Quote:
2.txt
chr1 21438731 21439423 26.12
chr1 33939851 33940673 34.76
chr1 36779864 36780494 20.16
chr1 36817091 36817917 27.22
chr2 36977015 36977908 19.27
chr3 40475125 40475885 21.58
chr3 40483838 40484616 15.3
chr4 40502827 40503675 10.61
chr4 40532299 40533156 14.78
chr5 43593022 43594143 24.33
...............................................
................................................
The following are my sequence of steps.

Quote:
This step makes a new file with each record in 1.txt against each record in 2.txt. The total records in 1_2.txt will be 10*10=100 records

awk 'NR==FNR{a[FNR]=$0;max2=FNR;next} {for (i=1;i<=max2;i++) print $0,a[i]}' 1.txt 2.txt > 1_2.txt
Quote:
This step compares if column1 matches column5 in 1_2.txt, because I don't want those records that has different chr names. Also, please note that I don't need the column5 again in my output.

awk '{if($1==$5) {print $1"\t"$2"\t"$3"\t"$4"\t"$6"\t"$7"\t"$8}}' 1_2.txt > test.tmp && mv test.tmp 1_2.txt

Quote:
Subtracting column2 and column5 from the previous output and printing the whole record with the subtraction result in the last column into another file.

awk '{(v=$2-$5); {print $0"\t"v}}' 1_2.txt > 1_2_distance.txt
Quote:
Now, I want to see if the last column, the subtraction result is in the range of -5000 to 5000. and print the whole record into another file.

awk '{if($8>=-5000 && $8<=5000) {print $1"\t"$2"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8}}' 1_2_distance.txt > 1_2_distance_5K.txt
Can someone please let me know about how to make these bunch of steps into a single script so that I start the script with 1.txt and 2.txt, after execution gives me the final 1_2_distance_5K.txt file.

Thanks in advance.
 

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LEARN ABOUT REDHAT

dos2unix

dos2unix(1)						      General Commands Manual						       dos2unix(1)

NAME

       dos2unix - DOS/MAC to UNIX text file format converter

SYNOPSYS

       dos2unix [options] [-c convmode] [-o file ...] [-n infile outfile ...]

       Options:

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

DESCRIPTION

       This manual page documents dos2unix, the program that converts plain text files in DOS/MAC format to UNIX 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 dos2unix 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.

	      dos2unix

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

	      dos2unix a.txt b.txt

	      dos2unix -o a.txt b.txt

       Convert and replace a.txt in ASCII conversion mode.  Convert and replace b.txt in ISO conversion mode.  Convert	c.txt  from  Mac  to  Unix
       ascii format.

	      dos2unix a.txt -c iso b.txt

	      dos2unix -c ascii a.txt -c iso b.txt

	      dos2unix -c mac a.txt b.txt

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

	      dos2unix -k a.txt

	      dos2unix -k -o a.txt

       Convert a.txt and write to e.txt.

	      dos2unix -n a.txt e.txt

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

	      dos2unix -k -n a.txt e.txt

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

	      dos2unix a.txt -n b.txt e.txt

	      dos2unix -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.

	      dos2unix -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.

AUTHORS

       Benjamin Lin - <blin@socs.uts.edu.au>

       Bernd Johannes Wuebben (mac2unix mode) <wuebben@kde.org>

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

       unix2dos(1) mac2unix(1)

1995.03.31							   dos2unix v3.0						       dos2unix(1)
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