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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 DEBIAN

fstrcmp

fstrcmp(1)						      General Commands Manual							fstrcmp(1)

NAME

       fstrcmp - fuzzy comparison of strings

SYNOPSIS

       fstrcmp [ -p ] first-string second-string
       fstrcmp -w first-string second-string
       fstrcmp -a first-file second-file
       fstrcmp -s needle haystack...
       fstrcmp --version

DESCRIPTION

       The  fstrcmp command is used to make fuzzy comparisons between strings.	The "edit distance" between the strings is printed, with 0.0 mean-
       ing the strings are utterly un-alike, and 1.0 meaning the strings are identical.

       You may need to quote the string to insulate them from the shell.

OPTIONS

       The fstrcmp command understands the following options:

       -a

       --files-as-bytes
	       This option is used to compare two files as arrays of bytes.  See fmemcmp(3) for more information.

       -p

       --pair  This option is used to compare two strings as arrays of bytes.  This is the default.  See fstrcmp(3) for more information.

       -s

       --select
	       This option is used to select the closest needle from the provided haystack alternatives.  The  most  similar  (single)	choice	is
	       printed.  If none are particularly similar, nothing is printed.	See fstrcmp(3) for more information.  See below for example.

       -V

       --version
	       This option may be used to print the version of the fstrcmp command, and then exit.

       -w

       --wide-pair
	       This option is used to compare two multi-byte character strings.  See fstrcoll(3) for more information.

EXIT STATUS

       The fstrcmp command exits with status 1 on any error.  The fstrcmp command only exits with status 0 if there are no errors.

EXAMPLE

       The fstrcmp --select option may be used in a shell script to improve error messages.
	      case "$action" in
	      start)
		  start
		  ;;
	      stop)
		  stop
		  ;;
	      restart)
		  stop
		  start
		  ;;
	      *)
		  echo "$0: action "$action" unknown" 1>&2
		  guess=`fstrcmp --select "$action" stop start restart`
		  if [ "$guess" ]
		  then
		      echo "$0: did you mean "$guess" instead?" 1>&2
		  fi
		  exit 1
		  ;;
	      esac
       Thus, the error message frequently suggests the correct action in the face of simple finger problems on the command line.

SEE ALSO

       fstrcmp(3)
	       fuzzy comparison of strings

       fstrcoll(3)
	       fuzzy comparison of two multi-byte character strings

       fstrcmpi(3)
	       fuzzy comparison of strings, integer variation

COPYRIGHT

       fstrcmp version 0.4
       Copyright (C) 2009 Peter Miller
       Peter Miller <pmiller@opensource.org.au>

       The  comparison	code  is  derived  from the fuzzy comparison functions in GNU Gettext 0.17.  The GNU Gettext comparison functions were, in
       turn, derived from GNU Diff 2.7.

       Copyright (C) 1988-2009 Free Software Foundation

																	fstrcmp(1)
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