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Full Discussion: Find & Replace command - Fasta file
Top Forums UNIX for Dummies Questions & Answers Find & Replace command - Fasta file Post 302580353 by methyl on Thursday 8th of December 2011 08:21:14 AM
Old 12-08-2011
No doubt posssible in "awk" or "sed" or whatever.

Open logic Shell approach. Too slow for large files.

Code:
cat filename.txt | while read line
do
        echo "${line}"
        read line
        echo "${line}"|fold -w 1|while read char
        do
                if [ ! "${char}" = "C" ]
                then
                        char="-"
                fi
                echo "${char}\c"
        done
        echo ""
done

>Sequence1
------C------C--------
>Sequence2
--CC------C-----C-
>Sequence3
------C-----CC-----C---

 

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LEARN ABOUT OPENSOLARIS

noecho

echo(3XCURSES)						  X/Open Curses Library Functions					    echo(3XCURSES)

NAME

       echo, noecho - enable/disable terminal echo

SYNOPSIS

       cc [ flag... ] file... -I /usr/xpg4/include  -L	/usr/xpg4/lib 
	-R  /usr/xpg4/lib  -lcurses  [ library... ]

       c89 [ flag... ] file... -lcurses [ library... ]

       #include <curses.h>

       int echo(void);

       int noecho(void);

DESCRIPTION

       The  echo()  function enables Echo mode for the current screen. The noecho() function disables Echo mode for the current screen. Initially,
       curses software echo mode is enabled and hardware echo mode of the tty driver is disabled. The echo() and noecho() functions control  soft-
       ware echo only. Hardware echo must remain disabled for the duration of the application, else the behavior is undefined.

RETURN VALUES

       Upon successful completion, these functions return OK. Otherwise, they return ERR.

ERRORS

       No errors are defined.

ATTRIBUTES

       See attributes(5) for descriptions of the following attributes:

       +-----------------------------+-----------------------------+
       |      ATTRIBUTE TYPE	     |	    ATTRIBUTE VALUE	   |
       +-----------------------------+-----------------------------+
       |Interface Stability	     |Standard			   |
       +-----------------------------+-----------------------------+
       |MT-Level		     |Unsafe			   |
       +-----------------------------+-----------------------------+

SEE ALSO

       getch(3XCURSES), getstr(3XCURSES), initscr(3XCURSES), libcurses(3XCURSES), scanw(3XCURSES), attributes(5), standards(5)

SunOS 5.11							    5 Jun 2002							    echo(3XCURSES)
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