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sorting based on alternative lines

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Top Forums Shell Programming and Scripting sorting based on alternative lines
# 1  
Old 08-23-2011
sorting based on alternative lines
Hello,

I have a file with multiple entries.

Code:
@SFGF-GA2-1_58:5:36:11009:999#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SFGF-GA2-1_58:5:36:11009:999#0/1
################################################################################
@SFGF-GA2-1_58:5:36:14498:999#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+SFGF-GA2-1_58:5:36:14498:999#0/1
################################################################################
@SFGF-GA2-1_58:5:36:3395:1010#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

I just want lines that start with @SFGF and the following line after it.

o/p

Code:
@SFGF-GA2-1_58:5:36:11009:1110#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
@SFGF-GA2-1_58:5:36:14498:999#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
@SFGF-GA2-1_58:5:36:14498:999#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
@SFGF-GA2-1_58:5:36:3395:1010#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

after this the file should be sorted based on @SFGF line.

o/p
Code:
@SFGF-GA2-1_58:5:36:14498:999#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
@SFGF-GA2-1_58:5:36:14498:999#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
@SFGF-GA2-1_58:5:36:3395:1010#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
@SFGF-GA2-1_58:5:36:11009:1110#0/1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN

Thanks,
# 2  
Old 08-23-2011
Code:
 sed -n '/^@SFGF/{N;p;}' Inp_File

# 3  
Old 08-23-2011
Could you fill in some of that NNNNN stuff? We need to see where you want it to end up too. And that line of ##### disappears mysteriously.
# 4  
Old 08-23-2011
Code:
awk '/^@SFGF/{print;getline;print}' file

What is the sort key for this data?
# 5  
Old 08-23-2011
first file

Code:
@SFGF-GA2-1_58:5:36:11009:999#0/1
ATGCATGCATGCATGCATAGGCATAGATAGACAGATACAGATATAGACATAGACATAGAAATATAT
+SFGF-GA2-1_58:5:36:11009:999#0/1
################################################################################
@SFGF-GA2-1_58:5:36:14498:1110#0/1
ATGGCGCTTTGCGTGGGCGTTTGACGAAGTTTGGGACCAGGGATAGCAGAAAATTTGACATAGACAT
+SFGF-GA2-1_58:5:36:14498:999#0/1
################################################################################
@SFGF-GA2-1_58:5:36:3395:1010#0/1
ATGCATGCCCCGTTTTAAACCGTTTGAAATTGCDCATGGATTTAGGGACCCATTGACCCATTACAATA
+SFGF-GA2-1_58:5:36:3395:1010#0/1
################################################################################

o/p

second file
[CODE]@SFGF-GA2-1_58:5:36:11009:999#0/1
ATGCATGCATGCATGCATAGGCATAGATAGACAGATACAGATATAGACATAGACATAGAAATATAT
@SFGF-GA2-1_58:5:36:14498:1110#0/1
ATGGCGCTTTGCGTGGGCGTTTGACGAAGTTTGGGACCAGGGATAGCAGAAAATTTGACATAGACAT
@SFGF-GA2-1_58:5:36:3395:1010#0/1
ATGCATGCCCCGTTTTAAACCGTTTGAAATTGCDCATGGATTTAGGGACCCATTGACCCATTACAATA

second o/p

Code:
@SFGF-GA2-1_58:5:36:11009:999#0/1
ATGCATGCATGCATGCATAGGCATAGATAGACAGATACAGATATAGACATAGACATAGAAATATAT
@SFGF-GA2-1_58:5:36:3395:1010#0/1
ATGCATGCCCCGTTTTAAACCGTTTGAAATTGCDCATGGATTTAGGGACCCATTGACCCATTACAATA
@SFGF-GA2-1_58:5:36:14498:1110#0/1
ATGGCGCTTTGCGTGGGCGTTTGACGAAGTTTGGGACCAGGGATAGCAGAAAATTTGACATAGACAT

# 6  
Old 08-23-2011
Try:
Code:
perl -ln0e '$,="\n";print sort {(split /:|#/, $a)[4]<=>(split /:|#/, $b)[4]} /^\@SFGF.*\n.*/mg;' file

# 7  
Old 08-23-2011
Thanks for the reply.

Its throwing an error

"panic: pp_match start/end pointers at -e line 1, <> chunk 1."

is it perl -lne?
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