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Full Discussion: Check group consistencies
Top Forums UNIX for Dummies Questions & Answers Check group consistencies Post 302931053 by ritakadm on Friday 9th of January 2015 07:39:58 PM
Old 01-09-2015
Check group consistencies
hello masters ,

please help here. I have 4 cols, I am looking for consistent 'geno' values within
'line', 'part' combinations. If the geno values are not consistent within a 'line', 'part' block, then we delete that block. One of the complications is that geno values are always 2 character, but AT and TA mean the same thing,similarly CG=GC etc.

I have 2 requests

1) Convert all 'geno' values in the whole dataset like AT and TA to either one or the other. I dont care which one, as long as they are consistent across the whole dataset.
2) Delete inconsistent 'line', 'part' combinations (red) from the data. If it is consistent (green) then just keep any one, in the example I have kept the first one.

Code:
line part serial geno
ax211 part1 1234 AA
gf345  part1 1345 TT
gf345  part1  3456 AA
gf345  part1 1346 TT
ax211 part2 1834 AA
gf345  part2 1395 TT
gf345  part2  3656 AA
gf345  part2 13746 TT
ax211 part3 1634 AA
gf345  part3 13345 AT
gf345  part3  34256 TA
gf345  part3 13446 AT

expected output

Code:
line part serial geno
ax211 part1 1234 AA
ax211 part2 1834 AA
ax211 part3 1634 AA
gf345  part3 13345 AT

For the first part I can try the following

Code:
sed "s/TA/AT/g;s/TC/CT/g;s/TG/GT/g;s/GC/CG/g;s/GA/AG/g;s/CA/AC/g;" file

but is there a smarter way to do this?

for the second part this is what I tried,

Code:
awk     'FNR==NR        {a[$1$2]+=$4;  b[$1$2]=$4;next}
                    $1$2 in b  {if (a[$1$2] ==1 ) print $0 }
        ' file file

 

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LEARN ABOUT DEBIAN

colorgccrc

COLORGCCRC(5)							File Formats Manual						     COLORGCCRC(5)

NAME

       colorgccrc - configuration file for colorgcc

DESCRIPTION

       A colorgccrc configuration file is used to configure the highlighting of the compiler output from colorgcc.

SYNTAX

       Each  line  consists  of  a  keyword  designating  a configuration variable.  The keyword is followed by `:' and then one or several values
       (depending on the keyword).  Lines beginning with a hash mark `#' are comments.

CONFIGURATION VARIABLES

       g++ | gcc | c++ | cc | g77 | gcj | gnat | gpc
	      Specifies the paths to the compilers.  Takes one value; a path to the compiler.

       nocolor
	      Specifies what terminal types colorization should be disabled on.  Takes one or several values, separated by whitespace.

       srcColor
	      Specifies the highlighting attributes source-code should be given.  Takes one or several color attributes.  See  the  section  COLOR
	      ATTRIBUTES for more information.

       introColor
	      Specifies  the  highlighting  attributes	for normal compiler output.  Takes one or several color attributes.  See the section COLOR
	      ATTRIBUTES for more information.

       warningFileNameColor | errorFileNameColor
	      Specifies the highlighting attributes for the filename in a  warning  or	an  error,  respectively.   Takes  one	or  several  color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

       warningNumberColor | errorNumberColor
	      Specifies  the  highlighting  attributes	for  the  line-number  in a warning or an error, respectively.	Takes one or several color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

       warningMessageColor | errorMessageColor
	      Specifies the highlighting attributes for the message-text in a warning or an error,  respectively.   Takes  one	or  several  color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

COLOR ATTRIBUTES

       The following attributes are valid for highlighting.

       clear, reset

       bold, underline, underscore, blink, reverse, concealed

       black, red, green, yellow, blue, magenta, cyan, white

       on_black, on_red, on_green, on_yellow, on_blue, on_magenta, on_cyan, on_white

SEE ALSO

       gcc(1), colorgcc(1)

HISTORY

       Jan 15 2003: Initial version of this manual-page.

REPORTING BUGS

       Report bugs to <jmoyers@geeks.com>

AUTHORS

       Jamie Moyers <jmoyers@geeks.com> is the author of colorgcc.

       This  manual  page  was	written  by Joe Wreschnig <piman@sacredchao.net>, and modified by David Weinehall <tao@debian.org>, for the Debian
       GNU/Linux system (but may be used by others).

COPYRIGHT

       Copyright (C) 2003 Jamie Moyers
       This is free software; see the source for copying conditions.  There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU-
       LAR PURPOSE.

								   Jan 15, 2003 						     COLORGCCRC(5)
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