Substitute newline with tab at designated field separator


 
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Old 04-02-2013
Substitute newline with tab at designated field separator

Hello, I need to replace newline with tab at certain lines of the file (every four lines is a record).
Code:
infile.fq:

@GAIIX-300
ATAGTCAAAT
+
_SZS^\\\cd
@GAIIX-300
CATACGACAT
+
hhghfdffhh
@GAIIX-300
GACGACGTAT
+
gggfc[hh]f

Code:
outfile:

@GAIIX-300    ATAGTCAAAT    +    _SZS^\\\cd
@GAIIX-300    CATACGACAT    +    hhghfdffhh
@GAIIX-300    GACGACGTAT    +    gggfc[hh]f

I used
Code:
 sed '/^@/N;/^@/N;/^@/N;s/\n/\t/g' infile.fq

without full understanding. I figured out this oneliner when I tried to understand newline substitution in sed.
1) Can anyone explain the three consecutive /^@/N; or N; which works too, for me (mean next line right)?
2) How can I use another command tr to do the job like:
Code:
!\n@ | tr  '\n' '\t' < infile.fq > outfile.tab

by adding the condition !\n@ to filter the record separator, which is @ here? I know awk can do the job much easier with RS="@", OFS="\t",
Code:
awk 'BEGIN{RS="@"; OFS="\t"} {print $1, $2, $3, $4}' infile.fq

but I want to understand how sed and tr work, if they can, in this case.
Thanks a lot!
YF

Last edited by yifangt; 04-02-2013 at 07:00 PM..
 
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