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[Solved] File reformat

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# 1  
Old 02-01-2014
[Solved] File reformat
I am using the code below to reformat the input (hp.txt). The output (newhp.txt) is not in the desired format and I can not seem to figure it out. I have attached both. Thank you.

Code:
 perl -aF/\\t/ -lne 'print join(" ",@F[0,1,2,$_,5]) for ("0 A","0 G","0 C","0 T","A 0","G 0","C 0","T 0")' hp.txt > newhp.txt

So in hp.txt the file looks like:
Code:
2    39224622    3922462       -       T         intron_7homopolymer
3    12632440    12632440     -        C        CDS_4homopolymer

Desired Output of newhp.txt
Code:
2  39224622  39224622   0   A  intron_7homopolymer 
2  39224622  39224622   0   T intron_7homopolymer
2  39224622  39224622   0   C intron_7homopolymer
2  39224622  39224622   0   G intron_7homopolymer
2  39224622  39224622   A   0 intron_7homopolymer
2  39224622  39224622   T   0 intron_7homopolymer
2  39224622  39224622   C   0 intron_7homopolymer
2  39224622  39224622   G   0 intron_7homopolymer
3  12632440  12632440   0   A CDS_4homopolymer
3  12632440  12632440   0   T CDS_4homopolymer
3  12632440  12632440   0   C CDS_4homopolymer
3  12632440  12632440   0   G CDS_4homopolymer
3  12632440  12632440   A   0 CDS_4homopolymer
3  12632440  12632440   T   0 CDS_4homopolymer
3  12632440  12632440   C   0 CDS_4homopolymer
3  12632440  12632440   G   0 CDS_4homopolymer

hp.txt (61.2 KB) 
newhp.txt (475.4 KB) 
Last edited by bartus11; 02-01-2014 at 11:30 AM.. Reason: Please use [code][/code] tags for input and output data.
# 2  
Old 02-01-2014
Try:
Code:
perl -ne 'for $i ("0 A","0 G","0 C","0 T","A 0","G 0","C 0","T 0") {$x=$_;$x=~s/-\t\w\t/$i\t/;print $x}' hp.txt > newhp.txt

# 3  
Old 02-01-2014
file reformat
Seemed to do the trick, but can the output be tab-delimineted?

1 115251260 115251260 0 A CDS_4homopolymer

Thanks.
newhp.txt (489.4 KB) 
# 4  
Old 02-01-2014
Code:
perl -ne 'for $i ("0\tA","0\tG","0\tC","0\tT","A\t0","G\t0","C\t0","T\t0") {$x=$_;$x=~s/-\t\w\t/$i\t/;print $x}' hp.txt > newhp.txt

This User Gave Thanks to bartus11 For This Post:
cmccabe
# 5  
Old 02-01-2014
file reformat
Thank you very much.
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