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Top Forums Shell Programming and Scripting Process alternate lines in awk/sed/perl Post 302832421 by empyrean on Sunday 14th of July 2013 11:06:37 PM
Old 07-15-2013
Process alternate lines in awk/sed/perl

hi..

i have a fasta file with the following format

Code:
>sequence1
CCGGTTTTCGATTTGGTTTGACT
>sequence2
AAAGTGCCGCCAGGTTTTGAGTGT
>sequence3
AGTGCCGCAGAGTTTGTAGTGT

Now, i want to read alternate line and add "GGGGGGGGGGG" to end of every sequence

Desired output:

Code:
>sequence1
CCGGTTTTCGATTTGGTTTGACTGGGGGGGGGGG
>sequence2
AAAGTGCCGCCAGGTTTTGAGTGTGGGGGGGGGGG
>sequence3
AGTGCCGCAGAGTTTGTAGTGTGGGGGGGGGGG

Moderator's Comments:
Mod Comment Please use CODE tags to mark code, input, and output samples.


---------- Post updated at 11:06 PM ---------- Previous update was at 11:00 PM ----------

---------- Post updated at 11:06 PM ---------- Previous update was at 11:06 PM ----------

I was trying the following command and missed a simple flower brace and struggling. Now i figured it out and working fine.. thanks..
Code:
awk 'NR % 2 {print} !(NR % 2) {print $0"GGGGGGGGG"}' seq.fa


Last edited by Don Cragun; 07-15-2013 at 12:04 AM.. Reason: Add CODE tags
 

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Locale::Script(3perl)					 Perl Programmers Reference Guide				     Locale::Script(3perl)

NAME
Locale::Script - standard codes for script identification SYNOPSIS
use Locale::Script; $script = code2script('phnx'); # 'Phoenician' $code = script2code('Phoenician'); # 'Phnx' $code = script2code('Phoenician', LOCALE_CODE_NUMERIC); # 115 @codes = all_script_codes(); @scripts = all_script_names(); DESCRIPTION
The "Locale::Script" module provides access to standards codes used for identifying scripts, such as those defined in ISO 15924. Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default ISO 15924 four-letter codes will be used. SUPPORTED CODE SETS
There are several different code sets you can use for identifying scripts. The ones currently supported are: alpha This is a set of four-letter (capitalized) codes from ISO 15924 such as 'Phnx' for Phoenician. This code set is identified with the symbol "LOCALE_SCRIPT_ALPHA". The Zxxx, Zyyy, and Zzzz codes are not used. This is the default code set. numeric This is a set of three-digit numeric codes from ISO 15924 such as 115 for Phoenician. This code set is identified with the symbol "LOCALE_SCRIPT_NUMERIC". ROUTINES
code2script ( CODE [,CODESET] ) script2code ( NAME [,CODESET] ) script_code2code ( CODE ,CODESET ,CODESET2 ) all_script_codes ( [CODESET] ) all_script_names ( [CODESET] ) Locale::Script::rename_script ( CODE ,NEW_NAME [,CODESET] ) Locale::Script::add_script ( CODE ,NAME [,CODESET] ) Locale::Script::delete_script ( CODE [,CODESET] ) Locale::Script::add_script_alias ( NAME ,NEW_NAME ) Locale::Script::delete_script_alias ( NAME ) Locale::Script::rename_script_code ( CODE ,NEW_CODE [,CODESET] ) Locale::Script::add_script_code_alias ( CODE ,NEW_CODE [,CODESET] ) Locale::Script::delete_script_code_alias ( CODE [,CODESET] ) These routines are all documented in the Locale::Codes man page. SEE ALSO
Locale::Codes Locale::Constants http://www.unicode.org/iso15924/ Home page for ISO 15924. AUTHOR
See Locale::Codes for full author history. Currently maintained by Sullivan Beck (sbeck@cpan.org). COPYRIGHT
Copyright (c) 1997-2001 Canon Research Centre Europe (CRE). Copyright (c) 2001-2010 Neil Bowers Copyright (c) 2010-2011 Sullivan Beck This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself. perl v5.14.2 2011-09-26 Locale::Script(3perl)
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