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Full Discussion: parsing data and incorporating it into another file
Top Forums Shell Programming and Scripting parsing data and incorporating it into another file Post 302435497 by Lucky Ali on Wednesday 7th of July 2010 01:14:55 PM
Old 07-07-2010
Hi,

I tried it. But it is only giving me what I wanted

This is the result I got

Code:
awk 'NR==FNR{a[">"$1]=$2;next}a[$1]{$0=$0 FS a[$1]}1' test1.fasta test2.fasta 
AB_1      gi|229194403|ref|ZP_04321208.1| 
AB_2      gi|229194404|ref|ZP_04321209.1|
AB_3      gi|229194405|ref|ZP_04321210.1|
AB_4      gi|229194406|ref|ZP_04321211.1| 
AB_5      gi|229194407|ref|ZP_04321212.1|

which is exactly similar to file2

I want the info in file 2 to be added to file 1 such that I will get a file like below;

Code:
>AB_1 gi|229194403|ref|ZP_04321208.1|
MLKKPIIIGVTGGSGGGKTSVSRAILDSFPNARIAMIQHDSYYKDQSHMSFEERVKTNYDHPLAFDTDFM
IQQLKELLAGRPVDIPIYDYKKHTRSNTTFRQDPQDVIIVEGILVLEDERLRDLMDIKLFVDTDDDIRII
RRIKRDMMERGRSLESIIDQYTSVVKPMYHQFIEPSKRYADIVIPEGVSNVVAIDVINSKIASILGEV
>AB_2 gi|229194404|ref|ZP_04321209.1|
MRARLIYNPTSGQELMRKSVPEVLDILEGFGYETSAFQTTAKKNSALNEARRAAKAGFDLLIAAGGDGTI
NEVVNGIAPLKKRPKMAIIPTGTTNDFARALKVPRGNPSQAAKLIGKNQTIQMDIGRAKKDTYFINIAAA
GSLTELTYSVPSQLKTMFGYLAYLAKGVELLPRVSNVPVKITHDKGVFEGQVSMIFAAITNSVGGFEMIA
PDAKLDDGMFTLILIKTANLFEIVHLLRLILDGGKHITDRRVEYIKTSKIVIEPQCGKRMMINLDGEYGG
DAPITLENLKNHITFFADTDLISDDALVLDQDELEIEEIVKKFAHEVEDLEQELEE
>AB_3 gi|229194405|ref|ZP_04321210.1|
MTGYDDFNYALSALKLGADDYLLKPFSKADVEDMLGKLRKKLELSKKTETIQELVEQPQKEVSAIAMAIH
ERLADSDLTLKSLAQQLGFSPNYLSVLIKKELGMPFQDYLVQERLKKAKLFLLTSNLKIYEIAEQVGFED
MNYFSQRFKQLVGVTPSQYKKGGQA

Please let me know
 

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LEARN ABOUT SUSE

git-symbolic-ref

GIT-SYMBOLIC-REF(1)						    Git Manual						       GIT-SYMBOLIC-REF(1)

NAME

       git-symbolic-ref - Read and modify symbolic refs

SYNOPSIS

       git symbolic-ref [-q] [-m <reason>] <name> [<ref>]

DESCRIPTION

       Given one argument, reads which branch head the given symbolic ref refers to and outputs its path, relative to the .git/ directory.
       Typically you would give HEAD as the <name> argument to see which branch your working tree is on.

       Given two arguments, creates or updates a symbolic ref <name> to point at the given branch <ref>.

       A symbolic ref is a regular file that stores a string that begins with ref: refs/. For example, your .git/HEAD is a regular file whose
       contents is ref: refs/heads/master.

OPTIONS

       -q, --quiet
	   Do not issue an error message if the <name> is not a symbolic ref but a detached HEAD; instead exit with non-zero status silently.

       -m
	   Update the reflog for <name> with <reason>. This is valid only when creating or updating a symbolic ref.

NOTES

       In the past, .git/HEAD was a symbolic link pointing at refs/heads/master. When we wanted to switch to another branch, we did ln -sf
       refs/heads/newbranch .git/HEAD, and when we wanted to find out which branch we are on, we did readlink .git/HEAD. This was fine, and
       internally that is what still happens by default, but on platforms that do not have working symlinks, or that do not have the readlink(1)
       command, this was a bit cumbersome. On some platforms, ln -sf does not even work as advertised (horrors). Therefore symbolic links are now
       deprecated and symbolic refs are used by default.

       git symbolic-ref will exit with status 0 if the contents of the symbolic ref were printed correctly, with status 1 if the requested name is
       not a symbolic ref, or 128 if another error occurs.

AUTHOR

       Written by Junio C Hamano <gitster@pobox.com[1]>

GIT

       Part of the git(1) suite

NOTES

	1. gitster@pobox.com
	   mailto:gitster@pobox.com

Git 1.7.1							    07/05/2010						       GIT-SYMBOLIC-REF(1)
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