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Full Discussion: Getting non unique lines from concatenated files
Top Forums UNIX for Dummies Questions & Answers Getting non unique lines from concatenated files Post 302507666 by pawannoel on Thursday 24th of March 2011 12:15:58 PM
Old 03-24-2011
@Bartus:

I have the same task but the file format is different now.

Code:
levure5_SNP_Consensus_Calls.txt:SK1.scplasm1    6153    22    22    T    C    0.000000    h4,h10,h9,     5752    5588    7    5588    3    20    0    -1    
levure6_SNP_Consensus_Calls.txt:SK1.scplasm1    6153    22    22    T    C    0.000000    h4,h10,h9,     4046    3862    10    3862    5    18    0    -1    
levure7_SNP_Consensus_Calls.txt:SK1.scplasm1    6153    22    22    T    C    0.000000    h4,h10,h9,     2264    2184    2    2184    3    21    0    -1    
levure8_SNP_Consensus_Calls.txt:SK1.scplasm1    6153    22    22    T    C    0.000000    h4,h10,h9,     2606    2537    2    2537    4    21    0    -1    
levure5_SNP_Consensus_Calls.txt:SK1.chr10    213804    13    13    G    A    0.999999    h3,     296    232    48    232    15    15    0    -1    
levure6_SNP_Consensus_Calls.txt:SK1.chr10    213804    13    13    G    A    1.000000    h3,     240    183    46    183    15    15    0    -1    
levure7_SNP_Consensus_Calls.txt:SK1.chr10    213804    13    13    G    A    0.000000    h3,     96    77    14    77    12    17    0    -1    
levure8_SNP_Consensus_Calls.txt:SK1.chr10    213804    13    13    G    A    1.000000    h3,     133    106    23    106    19    20    0    -1    
levure5_SNP_Consensus_Calls.txt:SK1.chrm    58283    10    10    C    T    0.000000    h4,h10,h9,     232    219    0    219    0    14    0    -1    
levure6_SNP_Consensus_Calls.txt:SK1.chrm    58283    10    10    C    T    0.000000    h4,h10,h9,     298    267    0    267    0    12    0    -1

I need to count number of A, T, G and C in 5th field and report as for example of above my expected output is:
Code:
T=4
G=4
C=2

Can you please provide both awk and perl versions, so that I can understand the difference?

---------- Post updated at 11:15 AM ---------- Previous update was at 11:05 AM ----------

I have used a primitive way of doing it foreach case like the following:

Code:
awk '{print $5}' file | sort | grep "A" | wc

But I'm sure there is a better way.

Cheers Smilie
 

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LEARN ABOUT REDHAT

mac2unix

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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