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Full Discussion: Awk script
Top Forums Shell Programming and Scripting Awk script Post 302498797 by ctsgnb on Tuesday 22nd of February 2011 12:55:37 PM
Old 02-22-2011
Code:
while IFS='=;' read a b c d e; do if [[ "$b" != "$d" ]]; then [[ "$f" ==  1 ]] && v=$d; f=0; b=$v; else f=1; fi; [[ ! -z $e ]] &&  d="$d;$e"; echo "$a=$b;$c=$d"; done <tst

Code:
# cat tst
sscaffold_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
scaffold_1      phytozome6      gene    19769   22804   .       +       .       ID=POPTR_0001s00210;Name=POPTR_0001s00210
scaffold_1      phytozome6      mRNA    19769   22804   .       +       .       ID=PAC:18238552;Name=POPTR_0001s00210.1;PACid=18238552;Parent=POPTR_0001s00210
scaffold_1      phytozome6      5'-UTR  19769   19827   .       +       .       Parent=PAC:18238552;PACid=18238552
scaffold_1      phytozome6      CDS     19828   20136   .       +       0       Parent=PAC:18238552;PACid=18238552
scaffold_1      phytozome6      CDS     22190   22516   .       +       0       Parent=PAC:18238552;PACid=18238552
scaffold_1      phytozome6      3'-UTR  22517   22804   .       +       .       Parent=PAC:18238552;PACid=18238552
scaffold_1      phytozome6      gene    74076   75893   .       +       .       ID=POPTR_0001s00220;Name=POPTR_0001s00220
scaffold_1      phytozome6      mRNA    74076   75893   .       +       .       ID=PAC:18237390;Name=POPTR_0001s00220.1;PACid=18237390;Parent=POPTR_0001s00220
scaffold_1      phytozome6      CDS     74076   74235   .       +       0       Parent=PAC:18237390;PACid=18237390
scaffold_1      phytozome6      CDS     74359   74634   .       +       2       Parent=PAC:18237390;PACid=18237390
scaffold_1      phytozome6      CDS     75259   75893   .       +       2       Parent=PAC:18237390;PACid=18237390
scaffold_1      phytozome6      gene    80191   81289   .       -       .       ID=POPTR_0001s00230;Name=POPTR_0001s00230
scaffold_1      phytozome6      mRNA    80191   81289   .       -       .       ID=PAC:18235601;Name=POPTR_0001s00230.1;PACid=18235601;Parent=POPTR_0001s00230
scaffold_1      phytozome6      CDS     81161   81289   .       -       0       Parent=PAC:18235601;PACid=18235601
scaffold_1      phytozome6      CDS     80191   80385   .       -       0       Parent=PAC:18235601;PACid=18235601
#

Code:
# while IFS='=;' read a b c d e; do if [[ "$b" != "$d" ]]; then [[ "$f" == 1 ]] && v=$d; f=0; b=$v; else f=1; fi; [[ ! -z $e ]] && d="$d;$e"; echo "$a=$b;$c=$d"; done <tst
sscaffold_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
scaffold_1      phytozome6      gene    19769   22804   .       +       .       ID=POPTR_0001s00210;Name=POPTR_0001s00210
scaffold_1      phytozome6      mRNA    19769   22804   .       +       .       ID=POPTR_0001s00210.1;Name=POPTR_0001s00210.1;PACid=18238552;Parent=POPTR_0001s00210
scaffold_1      phytozome6      5'-UTR  19769   19827   .       +       .       Parent=POPTR_0001s00210.1;PACid=18238552
scaffold_1      phytozome6      CDS     19828   20136   .       +       0       Parent=POPTR_0001s00210.1;PACid=18238552
scaffold_1      phytozome6      CDS     22190   22516   .       +       0       Parent=POPTR_0001s00210.1;PACid=18238552
scaffold_1      phytozome6      3'-UTR  22517   22804   .       +       .       Parent=POPTR_0001s00210.1;PACid=18238552
scaffold_1      phytozome6      gene    74076   75893   .       +       .       ID=POPTR_0001s00220;Name=POPTR_0001s00220
scaffold_1      phytozome6      mRNA    74076   75893   .       +       .       ID=POPTR_0001s00220.1;Name=POPTR_0001s00220.1;PACid=18237390;Parent=POPTR_0001s00220
scaffold_1      phytozome6      CDS     74076   74235   .       +       0       Parent=POPTR_0001s00220.1;PACid=18237390
scaffold_1      phytozome6      CDS     74359   74634   .       +       2       Parent=POPTR_0001s00220.1;PACid=18237390
scaffold_1      phytozome6      CDS     75259   75893   .       +       2       Parent=POPTR_0001s00220.1;PACid=18237390
scaffold_1      phytozome6      gene    80191   81289   .       -       .       ID=POPTR_0001s00230;Name=POPTR_0001s00230
scaffold_1      phytozome6      mRNA    80191   81289   .       -       .       ID=POPTR_0001s00230.1;Name=POPTR_0001s00230.1;PACid=18235601;Parent=POPTR_0001s00230
scaffold_1      phytozome6      CDS     81161   81289   .       -       0       Parent=POPTR_0001s00230.1;PACid=18235601
scaffold_1      phytozome6      CDS     80191   80385   .       -       0       Parent=POPTR_0001s00230.1;PACid=18235601
#

In a multi-line display (more readable)
Code:
while IFS='=;' read a b c d e
do if [[ "$b" != "$d" ]]
        then [[ "$f" == 1 ]] && v=$d; f=0; b=$v
        else f=1
fi
[[ ! -z $e ]] && d="$d;$e"
echo "$a=$b;$c=$d"
done <tst


Last edited by ctsgnb; 02-22-2011 at 02:22 PM..
This User Gave Thanks to ctsgnb For This Post:
 

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