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Full Discussion: Uppercase/lowercase comparison of one character per line with awk??
Top Forums Shell Programming and Scripting Uppercase/lowercase comparison of one character per line with awk?? Post 302385023 by ivpz on Thursday 7th of January 2010 01:32:08 AM
Old 01-07-2010
Uppercase/lowercase comparison of one character per line with awk??
Another frustrating scripting problem from a biologist trying to manipulate a file with several millions line. For each of the line I need to compare the uppercase A or C or G or T with the lowercase a or c or g or t. If there are more uppercases, a + should be added to a new column, otherwise a - is added. Many of the lines are duplicated or even triplicated, etc... This is to allow the comparison of only one character at a time in the order of ACGT. And to make it even more complicated, comparison on the last line of the repeated lines should be between the . and , where if there are more . than , a + should be added.

Below are the examples of some of my data. The columns with numbers are the count of uppercase ACGT and lowercase acgt respectively.
Code:
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0

And this is what I'll like to get:
Code:
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0  +
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0  +
.......GGGG,.G,,G...G.,.T...G.,..,.,,^F, 0 0 8 1 0 0 0 0  +
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0  -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0  -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0  -
,gc,,cga,g,c,,,,,,, 0 0 0 0 1 3 3 0  -
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0  +
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0  -
.....,,..,,...,,......,...cA.c,cC. 1 1 0 0 0 3 0 0  +

I've tried awk with if conditions but I guess it is too simple. Any suggestions or help will be very much appreciated!
Last edited by Scott; 01-07-2010 at 02:38 AM.. Reason: Added code tags
 

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LEARN ABOUT OPENDARWIN

uniq

UNIQ(1) 						    BSD General Commands Manual 						   UNIQ(1)

NAME

     uniq -- report or filter out repeated lines in a file

SYNOPSIS

     uniq [-c | -d | -u] [-i] [-f num] [-s chars] [input_file [output_file]]

DESCRIPTION

     The uniq utility reads the specified input_file comparing adjacent lines, and writes a copy of each unique input line to the output_file.	If
     input_file is a single dash ('-') or absent, the standard input is read.  If output_file is absent, standard output is used for output.  The
     second and succeeding copies of identical adjacent input lines are not written.  Repeated lines in the input will not be detected if they are
     not adjacent, so it may be necessary to sort the files first.

     The following options are available:

     -c      Precede each output line with the count of the number of times the line occurred in the input, followed by a single space.

     -d      Only output lines that are repeated in the input.

     -f num  Ignore the first num fields in each input line when doing comparisons.  A field is a string of non-blank characters separated from
	     adjacent fields by blanks.  Field numbers are one based, i.e. the first field is field one.

     -s chars
	     Ignore the first chars characters in each input line when doing comparisons.  If specified in conjunction with the -f option, the
	     first chars characters after the first num fields will be ignored.  Character numbers are one based, i.e. the first character is
	     character one.

     -u      Only output lines that are not repeated in the input.

     -i      Case insensitive comparison of lines.

DIAGNOSTICS

     The uniq utility exits 0 on success, and >0 if an error occurs.

COMPATIBILITY

     The historic +number and -number options have been deprecated but are still supported in this implementation.

SEE ALSO

     sort(1)

STANDARDS

     The uniq utility is expected to be IEEE Std 1003.2 (``POSIX.2'') compatible.

HISTORY

     A uniq command appeared in Version 3 AT&T UNIX.

BSD
								   June 6, 1993 							       BSD
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