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Thanks a lot guys.
I just did a slight modification to the awk code:
awk '{if (NR==1 && $0 ~/>/){print$0;next}if($0~/^>/){print"\n"$0;next}else{printf("%s",$0)}}'
As I was getting a extra newline...

Hello Friends,
Input File looks as follows:
>FASTA Header1
line1
line2
line3
linen
>FASTA Header2
Line1
Line2
linen
>FASTA Header3
and so on
.......

Output:
Want something as:...

Thanks everyone for your suggestions, I really wanted to make this work in AWK, but Perl codes are welcome. And many thanks for the code. I have not yet tried them, but will do now.
Cheers

Description of data:

NC_002737.1 4 F1VI4M001A3IAU F1VI4M001A3IAU F1VI4M001A3IAU F1VI4M001A3IAU
NC_006372.1 5 F1VI4M001BH0HY FF1VI4M001BH0HY F1VI4M001C0ZC5 F1VI4M001DOF2X F1VI4M001AYNTS...

How about breaking the file into multiple small files do the sort and merge them later.
As pointed out the disk is full, check with "du" in UNIX/Linux.
Try Perl/Python to do a intelligent sort,...

I have it working now...

Thanks, I really appreciate it.
There is one other thing. You have undef $\. Which is good if the file is small. But the files are going to grow and this is why I am trying to go line by line using...

Hi Tyler,
Hi did not quite get the regex you have said. Why is there a "bit" operator (|) in the regular expression ((Query= $x.*)Query=|(Query= $x.*)
The idea was IDs in File1 and lots of Stuff in...

[SIZE=2][SIZE=2]Hello People,
Need some assistance/guidance.
OUTLINE:
Two files (File1 and File2)
File1 has some ids such as
009463_3922_1827
897654_8764_5432
File2 has things...