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Generating a file based on another file

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# 1  
Old 07-07-2010
Generating a file based on another file
I am trying to generate a file like this one
Quote:
;1.0
1;2;3;4;5;6;7;8;9;10;11;12;13;14;15;16;17;18;19;20;
10;10;10;10;10;10;10;10;10;10;10;10;10;10;10;10;10;10;10;10;
>GHL8OVD01BNNCA Freq 4;1;;;;
TAGATGTGCCCGTGGGTTTC
>GHL8OVD01CMQVT Freq 15;1;;;;
TTGATGTCGTGGGTTTCCCG
>GHL8OVD01CMQVT Freq 50;1;;;;
TTGATGTGCCAGTTTCCCGT
>GHL8OVD01CMQVW Freq 700;1;;;;
TTGATGTGTCCCGTCGACAC
>GHL8OVD01A45V3 Freq 9;1;;;;
TTGATTCCCGTCGACACCGG
>GHL8OVD01AV2U9 Freq 17;1;;;;
TTGATGTGCCAGCTTTCGCG
Based on this other file
Quote:
>GHL8OVD01BNNCA Freq 4
TAGATGTGCCCGTGGGTTTC
>GHL8OVD01CMQVT Freq 15
TTGATGTCGTGGGTTTCCCG
>GHL8OVD01CMQVT Freq 50
TTGATGTGCCAGTTTCCCGT
>GHL8OVD01CMQVW Freq 700
TTGATGTGTCCCGTCGACAC
>GHL8OVD01A45V3 Freq 9
TTGATTCCCGTCGACACCGG
>GHL8OVD01AV2U9 Freq 17
TTGATGTGCCAGCTTTCGCG
The first part at the very top ( ;1.0) is a constant so it does not change from file to file -that part is not a problem. My problems start with the second line, as you can see those are consecutive numbers (1;2;3; etc) representing the length of those sequences (In this case 20, all sequences are the same length). Then, the 3rd line has 20 "10;" one after another, just like above the number of "10;" is = to the sequence length. The rest of the file is almost identical to the original with the only difference that I need to add a pattern to each ID (;1;;;Smilie. I need to do some manipulation afterwards but that part is pretty much taken care of.
Any help will be greatly appreciated.
Last edited by Xterra; 07-08-2010 at 12:02 PM..
# 2  
Old 07-08-2010
Try...
Code:
awk 'BEGIN {
          n = 20
          for (i = 1; i <= n; i++) {
               x = x i ";"
               y = y "10;"
          }
          print ";1.0"
          print x
          print y
     }

     {
          if ($0 ~ /^>/)
               print $0 ";1;;;;"
          else
               print $0
     }
     ' file1 > file2

# 3  
Old 07-08-2010
Code:
awk 'NR==2{print length($0)}' file | awk 'BEGIN{getline;n=$0;print ";1.0";for (i=1;i<=n;i++) printf "%s;",i;
printf "\n";for (i=1;i<=n;i++) printf "10;";printf "\n"}!/^>/{sub("$",";1;;;;");print;next}1' - file

This User Gave Thanks to bartus11 For This Post:
Xterra
# 4  
Old 07-08-2010
Can you explain how you change
Code:
>GHL8OVD01BNNCA Freq 4
TAGATGTGCCCGTGGGTTTC

to

Code:
>GHL8OVD01BNNCA Freq 4;1;;;;
AGTGCCCGTGGGTTTC

The red parts have different length.
# 5  
Old 07-08-2010
bartus11
Thanks a lot!
I only need to chage where the pattern ";1;;;;" is being added. It should be next to the Freq value rather than the end of the sequence. I will try to modify your code accordingly.
Last edited by Xterra; 07-08-2010 at 12:42 PM..
# 6  
Old 07-08-2010
Just remove "!", so it looks like:
Code:
awk 'NR==2{print length($0)}' file | awk 'BEGIN{getline;n=$0;print ";1.0";for (i=1;i<=n;i++) printf "%s;",i;
printf "\n";for (i=1;i<=n;i++) printf "10;";printf "\n"}/^>/{sub("$",";1;;;;");print;next}1' - file

# 7  
Old 07-08-2010
My bad!
I had a problem with the input file and that's why it was not working when I tried without the "!".
Thanks!
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