Extract distinc sequence of letters Post: 302920977

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Top Forums Shell Programming and Scripting Extract distinc sequence of letters Post 302920977 by Don Cragun on Tuesday 14th of October 2014 03:45:30 AM

10-14-2014

Registered User

Quote:

Originally Posted by kamcamonty

Hallo,
I need to extract distinct sequence of letters for example from 136 to 193
Files are quite big, so I would prefer not to use "fold -w1"
Thank you very much

Input file look like this:

Code:

       1 cttttacctt catgtgtttt tgcagatatt tgttcataat aacatcttct ttttaagtta
      61 ttaaaatctt ttttaaagtt attaacattt ttttgtcttt tagatcctat atagatccta
      121 aaagatccta aaagatccta aaagatcccc gtttttgtta aagcatatgt gataaggttt
      181 tatagtactt taagattcac tatagtcagt aaaacgttca ctatagtcag taaaacgttc

I'm lost.

Please use CODE tags.
From 136 to 193 what? You have shown us lines with a variable length digit string followed by 5 or 6 groups of 10 letters. The only thing you have shown us between 136 and 193 is the digit string 181 marked in red above.
What do you mean by "Files are quite big"? How long will the longest lines be in your input files? What is the maximum size (in bytes) of your input files?
What output are you expecting from the above sample input?
I understand that you don't want to use fold -w1, but I don't understand why you would say that. I don't see how using fold -w1 to put each character in your input files on a single line would help solve this problem. (But, maybe that is just because I can't figure out what you're trying to do.)
What OS and shell are you using?

Last edited by Don Cragun; 10-14-2014 at 04:48 AM.. Reason: Add request for OS and shell information.

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LEARN ABOUT CENTOS

fold

FOLD(1) 							   User Commands							   FOLD(1)

NAME

       fold - wrap each input line to fit in specified width

SYNOPSIS

       fold [OPTION]... [FILE]...

DESCRIPTION

       Wrap input lines in each FILE (standard input by default), writing to standard output.

       Mandatory arguments to long options are mandatory for short options too.

       -b, --bytes
	      count bytes rather than columns

       -c, --characters
	      count characters rather than columns

       -s, --spaces
	      break at spaces

       -w, --width=WIDTH
	      use WIDTH columns instead of 80

       --help display this help and exit

       --version
	      output version information and exit

       GNU coreutils online help: <http://www.gnu.org/software/coreutils/> Report fold translation bugs to <http://translationproject.org/team/>

AUTHOR

       Written by David MacKenzie.

COPYRIGHT

       Copyright (C) 2013 Free Software Foundation, Inc.  License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO

       The  full documentation for fold is maintained as a Texinfo manual.  If the info and fold programs are properly installed at your site, the
       command

	      info coreutils 'fold invocation'

       should give you access to the complete manual.

GNU coreutils 8.22						     June 2014								   FOLD(1)

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