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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 302436206 by Lucky Ali on Friday 9th of July 2010 04:49:45 PM
Old 07-09-2010
Thanks Christoph Spohr for correcting me.

It worked for me.

I guess the awk would work when the file2 have characters with out space

Code:
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|

suppose if I have the above file with some more data separated by one or 2 spaces such as

Code:
AB_1      gi|229194403|ref|ZP_04321208.1| group II intron reverse transcriptase/maturase [asd ert 456]
AB_2      gi|229194404|ref|ZP_04321209.1|
AB_3      gi|229194405|ref|ZP_04321210.1|
AB_4      gi|229194406|ref|ZP_04321211.1| alkylphosphonate uptake protein [Bder ce 33L]
AB_5      gi|229194407|ref|ZP_04321212.1| hypothetical protein pE33L466_0459 [Badfr cereus 33L]

how do I modify the above awk command to parse the complete data.

Please let me know.

---------- Post updated at 04:49 PM ---------- Previous update was at 03:44 PM ----------

Hi All,
This is just to make my question much more clear.

It is a continuation of the awk code that had been previous suggested by Christoph Spohr and Franklin:

Code:
awk 'NR==FNR


Code:



{a[">"$1]=$2;next}a[$1]{$0=$0 FS a[$1]}1' test2.fasta test1.fasta

I found that if file 2 have more charatcers separated by space in it, the above mentioned awk code will only grab the characters until the space and move it to file1.

how would I modify the above awk so that all the characters in file 2 is parsed and placed on file1.

please let me know.

LA
 

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LEARN ABOUT CENTOS

git-symbolic-ref

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

NAME

       git-symbolic-ref - Read, modify and delete symbolic refs

SYNOPSIS

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

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>.

       Given --delete and an additional argument, deletes the given symbolic 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

       -d, --delete
	   Delete the symbolic ref <name>.

       -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.

       --short
	   When showing the value of <name> as a symbolic ref, try to shorten the value, e.g. from refs/heads/master to master.

       -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. But symbolic links are
       not entirely portable, so they are now deprecated and symbolic refs (as described above) 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.

GIT

       Part of the git(1) suite

Git 1.8.3.1							    06/10/2014						       GIT-SYMBOLIC-REF(1)
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