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Help with removing duplicate entries with awk or Perl

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# 15  
Old 10-29-2012
save the below code as a.awk
Code:
!($2 in a){printf("%s %s ",$1,$2);a[$2]}
!($3 in b){printf("%s ",$3);b[$3]}
!($5 in c){printf("%s %s ",$4,$5);c[$5]}
!($6 in d){printf("%s %s ",$5,$6);d[$6]}
!($7 in e){printf("%s ",$7);e[$7]}
!($9 in f){printf("%s %s ",$8,$9);f[$9]}
!($10 in g){printf("%s %s",$10,$11);g[$10]}
{printf("\n")}

execute the awk command by

Code:
awk -f a.awk input.txt

# 16  
Old 10-29-2012
Code:
$
$ cat input
chr1    11127067        11132181        89      chr1    11128023        11128311        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11128023        11128311        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11131908        11132010        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11131908        11132010        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11130992        11131108        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11130992        11131108        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11128311        11128447        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11128311        11128447        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11130630        11130711        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11130630        11130711        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11130729        11130979        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11130729        11130979        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11131263        11131553        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11131263        11131553        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11131587        11131709        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11131587        11131709        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11132034        11132488        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11132034        11132488        chr1    11131583        11131618        1
$
$
$ perl -F"\t" -lane 'for ($i=0; $i<=$#F; $i++) {
                       if (not defined $tokens{$i.":".$F[$i]}) {push @x, $F[$i]}
                       else {push @x, ""}
                     }
                     if (join("",@x) ne "") {
                       for ($i=0; $i<=$#x; $i++) { $line .= sprintf ("%-10s", $x[$i]) }
                       print $line;
                     }
                     for ($i=0; $i<=$#F; $i++) { $tokens{$i.":".$F[$i]}++ };
                     $line = ""; @x = ();
                    ' input
chr1      11127067  11132181  89        chr1      11128023  11128311  chr1      11130990  11131025  5
                                                                                11131583  11131618  1
                                                  11131908  11132010
                                                  11130992  11131108
                                                  11128311  11128447
                                                  11130630  11130711
                                                  11130729  11130979
                                                  11131263  11131553
                                                  11131587  11131709
                                                  11132034  11132488
$
$
$

tyler_durden
# 17  
Old 10-30-2012
Sorry it doesn't work
# 18  
Old 10-30-2012
try

Code:
awk '{for(i=1;i<=NF;i++){if(X[$i,i]++){$i=""}}}1' OFS="\t" file

# 19  
Old 10-30-2012
Doesn't work...I have attached the result as output.txt. Kindly have a look.
# 20  
Old 10-30-2012
Quote:
Originally Posted by Amit Pande
Doesn't work...I have attached the result as output.txt. Kindly have a look.
Your expected output doesn't replicate what you say.

please look

Code:
chr1    11127067    11132181    89    chr1    11128023    11128311    chr1    11130990    11131025    5
                        chr1    11131908    11132010    chr1    11131583    11131618    1
                        chr1    11130992    11131108    
                        chr1    11128311    11128447

Code:
duplicate lines in column 1,2,3,5,6,7,8,9,10 should be removed while those that are not duplicate lines should be retained.

1) From column 6 and 7 only 4 lines are printed in expected output.(you can see there few more)
2) See red chr1 this also duplicates.(why they are printed.
3) And if you don't want to consider column 4 it should be present for all the lines right.?

Assuming you don't want consider column 4 for duplicates.

Code:
$ cat file
chr1    11127067        11132181        89      chr1    11128023        11128311        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11128023        11128311        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11131908        11132010        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11131908        11132010        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11130992        11131108        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11130992        11131108        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11128311        11128447        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11128311        11128447        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11130630        11130711        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11130630        11130711        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11130729        11130979        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11130729        11130979        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11131263        11131553        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11131263        11131553        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11131587        11131709        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11131587        11131709        chr1    11131583        11131618        1
chr1    11127067        11132181        89      chr1    11132034        11132488        chr1    11130990        11131025        5
chr1    11127067        11132181        89      chr1    11132034        11132488        chr1    11131583        11131618        1

$ awk '{for(i=1;i<=NF;i++){if((X[$i,i]++) && i!=4){$i=""}}}1' OFS="\t" file
chr1    11127067        11132181        89      chr1    11128023        11128311        chr1    11130990        11131025        5
                        89                                      11131583        11131618        1
                        89              11131908        11132010
                        89
                        89              11130992        11131108
                        89
                        89              11128311        11128447
                        89
                        89              11130630        11130711
                        89
                        89              11130729        11130979
                        89
                        89              11131263        11131553
                        89
                        89              11131587        11131709
                        89
                        89              11132034        11132488
                        89

And considering all the columns..

Code:
]$ awk '{for(i=1;i<=NF;i++){if(X[$i,i]++){$i=""}}}1' OFS="\t" file
chr1    11127067        11132181        89      chr1    11128023        11128311        chr1    11130990        11131025        5
                                                                11131583        11131618        1
                                        11131908        11132010

                                        11130992        11131108

                                        11128311        11128447

                                        11130630        11130711

                                        11130729        11130979

                                        11131263        11131553

                                        11131587        11131709

                                        11132034        11132488

Hope this helps youSmilie

pamu
# 21  
Old 10-30-2012
Thanks a lot....this one works...but unfortunately..the first column is not reported for each entry...I have attached the output...kindly do through it..
Last edited by Amit Pande; 03-19-2013 at 02:30 PM..
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