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# 1  
Old 02-20-2011
MySQL Awk script
I have following text
Code:
scaffold_1      phytozome6      gene    12632   13612   .       +       .       ID=PT_0001s00200;Name=PT_0001s00200
scaffold_1      phytozome6      mRNA    12632   13612   .     +       .     ID=PAC:18235173;Name=PT_0001s00200.1;PACid=18235173;Parent=PT_0001s00200
scaffold_1      phytozome6      5'-UTR  12632   12638   .       +       .       Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      CDS     12639   12650   .       +       0      Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      CDS     12768   12891   .       +       0      Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      CDS     13117   13226   .       +       2      Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      CDS     13310   13384   .       +       0      Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      3'-UTR  13385   13612   .       +       .       Parent=PAC:18235173;PACid=18235173

I want convert into
Code:
scaffold_1      phytozome6      gene    12632   13612   .       +       .       ID=PT_0001s00200;Name=PT_0001s00200
scaffold_1      phytozome6      mRNA    12632   13612   .     +       .     ID=PT_0001s00200.1;Name=PT_0001s00200.1;PACid=18235173;Parent=PT_0001s00200
scaffold_1      phytozome6      5'-UTR  12632   12638   .       +       .       Parent=PT_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      CDS     12639   12650   .       +       0      Parent=PT_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      CDS     12768   12891   .       +       0      Parent=PT_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      CDS     13117   13226   .       +       2      Parent=PT_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      CDS     13310   13384   .       +       0      Parent=PT_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      3'-UTR  13385   13612   .       +       .       Parent=PT_0001s00200.1;PACid=18235173

I tried with following script
Code:
awk '{if(substr($9,17,10)=="Name=PT") print gensub("Parent=PAC:"substr($9,47,9),"Parent="substr($9,22,16)".1",
  substr($0,0)) substr($0,0) }' inputfile > outputfile

but still no luck.

Can you please help me,
Last edited by Scott; 02-20-2011 at 05:54 AM.. Reason: Please use code tags
# 2  
Old 02-20-2011
why not use sed?
Code:
sed 's/Parent=PAC:18235173;PACid=18235173/Parent=PT_0001s00200.1;PACid=18235173/g'

You can do an inline edit to the same file using the -i switch. Or redirect it to another file like your example shows
# 3  
Old 02-20-2011
I have used following script but still I cant replace the Parent=PAC
Code:
awk '{if(substr($9,17,10)=="Name=PT") n=substr($9,22,16) gsub("Parent=PAC:"substr($9,47,9),"Parent="n".1");
  gsub("ID=PAC:"substr($9,8,19),"ID="n".1");  }' input>output

any help appreciated

---------- Post updated at 04:50 AM ---------- Previous update was at 04:41 AM ----------

Thank you for your reply,but this is only one record there are set records with unique PAC and PT ids ,In this case I have to use your solution 300000 times with changing PAC and PT ids,cant we use
Code:
if(substr($9,17,10)=="Name=PT")

with your solution.
Last edited by Scott; 02-20-2011 at 05:55 AM.. Reason: Code tags
# 4  
Old 02-20-2011
Code:
awk -F"[=;]" 'NR==1{s=$2 ".1";print;FS=OFS=";";next}{sub(/=.*/,"="s,$1)}1' infile

# 5  
Old 02-20-2011
Thank you for your reply but I get following
Code:
scaffold_1      phytozome6      gene    2330052 2335284 .       -       .       ID=.1;Name=PT_0001s02940
scaffold_1      phytozome6      mRNA    2330052 2335284 .       -       .       ID=.1;Name=PT_0001s02940.1;PACid=18235154;Parent=PT_0001s02940
scaffold_1      phytozome6      CDS     2334981 2335230 .       -       0       Parent=.1;PACid=18235154
scaffold_1      phytozome6      5'-UTR  2335231 2335284 .       -       .       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2334079 2334206 .       -       2       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2333907 2333978 .       -       0       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2333635 2333780 .       -       0       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2333448 2333562 .       -       1       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2333285 2333365 .       -       0       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2332541 2332678 .       -       0       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2331826 2331913 .       -       0       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2330651 2330764 .       -       2       Parent=.1;PACid=18235154
scaffold_1      phytozome6      3'-UTR  2330052 2330460 .       -       .       Parent=.1;PACid=18235154
scaffold_1      phytozome6      CDS     2330461 2330483 .       -       2       Parent=.1;PACid=18235154

still no luck,
I used following command it will give the correct output,Did I do correct?
Code:
awk '{if(substr($9,1,5)=="ID=PT_") n=substr($9,4,16)".1"; gsub("ID=PAC:"substr($9,8,8),"ID="n);
  gsub("Parent=PAC:"substr($9,12,8),"Parent="n); print; }' infile > outfile

Last edited by Scott; 02-20-2011 at 12:46 PM.. Reason: Code tags
# 6  
Old 02-20-2011
is your document's first line different as the sample? I get the ID number from the first line.

The first line should be:

Code:
scaffold_1      phytozome6      gene    12632   13612   .       +       .       ID=PT_0001s00200;Name=PT_0001s00200

# 7  
Old 02-20-2011
yes It is different
Code:
scaffold_1      phytozome6      gene    12632   13612   .       +       .       ID=POPTR_0001s00200;Name=POPTR_0001s00200
scaffold_1      phytozome6      mRNA    12632   13612   .     +       .     ID=PAC:18235173;Name=POPTR_0001s00200.1;PACid=18235173;Parent=POPTR_0001s00200
scaffold_1      phytozome6      5'-UTR  12632   12638   .       +       .       Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      CDS     12639   12650   .       +       0      Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      CDS     12768   12891   .       +       0      Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      CDS     13117   13226   .       +       2      Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      CDS     13310   13384   .       +       0      Parent=PAC:18235173;PACid=18235173
scaffold_1      phytozome6      3'-UTR  13385   13612   .       +       .       Parent=PAC:18235173;PACid=18235173

change it to
Code:
caffold_1      phytozome6      gene    12632   13612   .       +       .       ID=POPTR_0001s00200;Name=POPTR_0001s00200
scaffold_1      phytozome6      mRNA    12632   13612   .     +       .     ID=POPTR_0001s00200.1;Name=POPTR_0001s00200.1;PACid=18235173;Parent=POPTR_0001s00200
scaffold_1      phytozome6      5'-UTR  12632   12638   .       +       .       Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      CDS     12639   12650   .       +       0      Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      CDS     12768   12891   .       +       0      Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      CDS     13117   13226   .       +       2      Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      CDS     13310   13384   .       +       0      Parent=POPTR_0001s00200.1;PACid=18235173
scaffold_1      phytozome6      3'-UTR  13385   13612   .       +       .       Parent=POPTR_0001s00200.1;PACid=18235173

Do you think your function will help.sorry for changing format
Last edited by Scott; 02-20-2011 at 12:46 PM..
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