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Column content match and add suffix

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# 1  
Old 05-31-2012
Column content match and add suffix
My input

Code:
chr3    galGal3_xenoRefFlat     CDS     4178235 4178264 0.000000        +       0       gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     exon    4178235 4178264 0.000000        +       .	gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     CDS     4178746 4178826 0.000000        +       0       gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     exon    4178746 4178826 0.000000        +       .       gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     CDS     4179277 4179338 0.000000        +       0       gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     exon    4179277 4179338 0.000000        +       .       gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     CDS     4184594 4184751 0.000000        +       0       gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     exon    4184594 4184751 0.000000        +       .	gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     CDS     4187403 4187538 0.000000        +       1	gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     exon    4187403 4187541 0.000000        +       .       gene_id "T6J4.19; T6J4_19"; transcript_id "T6J4.19; T6J4_19";
chr3    galGal3_xenoRefFlat     CDS     4179280 4179336 0.000000        +       0       gene_id "T15C9.2"; transcript_id "T15C9.2";
chr3    galGal3_xenoRefFlat     exon    4179280 4179336 0.000000        +       .	gene_id "T15C9.2"; transcript_id "T15C9.2";
chr3    galGal3_xenoRefFlat     CDS     4180045 4180087 0.000000        +       1	gene_id "AT3G26020"; transcript_id "AT3G26020_dup1";
chr3    galGal3_xenoRefFlat     exon    4180045 4180087 0.000000        +       .       gene_id "AT3G26020"; transcript_id "AT3G26020_dup1";
chr3    galGal3_xenoRefFlat     CDS     4187410 4187538 0.000000        +       0	gene_id "AT3G26020"; transcript_id "AT3G26020_dup1";
chr3    galGal3_xenoRefFlat     exon    4187410 4187541 0.000000        +       .       gene_id "AT3G26020"; transcript_id "AT3G26020_dup1";
chr3    galGal3_xenoRefFlat     CDS     4178746 4178876 0.000000        +       0	gene_id "si687042f02"; transcript_id "si687042f02";
chr3    galGal3_xenoRefFlat     exon    4178746 4178876 0.000000        +       .	gene_id "si687042f02"; transcript_id "si687042f02";

My output

Code:
chr3    galGal3_xenoRefFlat     CDS     4178235 4178264 0.000000        +       0       gene_id "T6J4.19_1"; transcript_id "T6J4.19_1";
chr3    galGal3_xenoRefFlat     exon    4178235 4178264 0.000000        +       .	gene_id "T6J4.19_2"; transcript_id "T6J4.19_2";
chr3    galGal3_xenoRefFlat     CDS     4178746 4178826 0.000000        +       0       gene_id "T6J4.19_2"; transcript_id "T6J4.19_3";
chr3    galGal3_xenoRefFlat     exon    4178746 4178826 0.000000        +       .       gene_id "T6J4.19_3"; transcript_id "T6J4.19_4";
chr3    galGal3_xenoRefFlat     CDS     4179277 4179338 0.000000        +       0       gene_id "T6J4.19_4"; transcript_id "T6J4.19_5";
chr3    galGal3_xenoRefFlat     exon    4179277 4179338 0.000000        +       .       gene_id "T6J4.19_5"; transcript_id "T6J4.19_6";
chr3    galGal3_xenoRefFlat     CDS     4184594 4184751 0.000000        +       0       gene_id "T6J4.19_6"; transcript_id "T6J4.19_7";
chr3    galGal3_xenoRefFlat     exon    4184594 4184751 0.000000        +       .	gene_id "T6J4.19_7"; transcript_id "T6J4.19_8";
chr3    galGal3_xenoRefFlat     CDS     4187403 4187538 0.000000        +       1	gene_id "T6J4.19_8"; transcript_id "T6J4.19_9";
chr3    galGal3_xenoRefFlat     exon    4187403 4187541 0.000000        +       .       gene_id "T6J4.19_9"; transcript_id "T6J4.19_10";
chr3    galGal3_xenoRefFlat     CDS     4179280 4179336 0.000000        +       0       gene_id "T15C9.2_1"; transcript_id "T15C9.2_1";
chr3    galGal3_xenoRefFlat     exon    4179280 4179336 0.000000        +       .	gene_id "T15C9.2_2"; transcript_id "T15C9.2_2";
chr3    galGal3_xenoRefFlat     CDS     4180045 4180087 0.000000        +       1	gene_id "AT3G26020_1"; transcript_id "AT3G26020_dup1_1";
chr3    galGal3_xenoRefFlat     exon    4180045 4180087 0.000000        +       .       gene_id "AT3G26020_2"; transcript_id "AT3G26020_dup1_2";
chr3    galGal3_xenoRefFlat     CDS     4187410 4187538 0.000000        +       0	gene_id "AT3G26020_3"; transcript_id "AT3G26020_dup1_3";
chr3    galGal3_xenoRefFlat     exon    4187410 4187541 0.000000        +       .       gene_id "AT3G26020_4"; transcript_id "AT3G26020_dup1_4";
chr3    galGal3_xenoRefFlat     CDS     4178746 4178876 0.000000        +       0	gene_id "si687042f02_1"; transcript_id "si687042f02_1";
chr3    galGal3_xenoRefFlat     exon    4178746 4178876 0.000000        +       .	gene_id "si687042f02_2"; transcript_id "si687042f02_2";

Basically, what I want to do is match the content of one row's gene_id and transcript_id which are separated by space to the other row. If they are the same, I would like to add a suffix as a series, i.e _1, _2...so on.

Please note that the columns are separated by spaces.

Thanks for ur help.
# 2  
Old 05-31-2012
I think you can do this in a awk one liner. This will basically just append a number corresponding to the number of times a value has appeared consecutively in each column.

Code:
awk '{ for(i=1; i<=NF; i++) { if($i == a[i] ) { k[i] = (k[i]+1); printf $i"_"k[i]" " } else { printf $i"_1 "; k[i]=1 } } print ""; split($0,a," ") }' input > output


Input:

Code:
A B C
A B C
A D E
B D E

Output:

Code:
A_1 B_1 C_1 
A_2 B_2 C_2 
A_3 D_1 E_1 
B_1 D_2 E_2

This User Gave Thanks to hydrabane For This Post:
jacobs.smith
# 3  
Old 06-01-2012
Hi hydrabane,

Thanks for ur valuable time.

Your code works, but it is printing the suffix for each and every column like this

Code:
chr3_1 galGal3_xenoRefFlat_1 CDS_1 4178235_1 4178264_1 0.000000_1 +_1 0_1 gene_id_1 "T6J4.19;_1 T6J4_19";_1 transcript_id_1 "T6J4.19;_1 T6J4_19";_1 
chr3_2 galGal3_xenoRefFlat_2 exon_1 4178235_2 4178264_2 0.000000_2 +_2 ._1 gene_id_2 "T6J4.19;_2 T6J4_19";_2 transcript_id_2 "T6J4.19;_2 T6J4_19";_2 
chr3_3 galGal3_xenoRefFlat_3 CDS_1 4178746_1 4178826_1 0.000000_3 +_3 0_1 gene_id_3 "T6J4.19;_3 T6J4_19";_3 transcript_id_3 "T6J4.19;_3 T6J4_19";_3 
chr3_4 galGal3_xenoRefFlat_4 exon_1 4178746_2 4178826_2 0.000000_4 +_4 ._1 gene_id_4 "T6J4.19;_4 T6J4_19";_4 transcript_id_4 "T6J4.19;_4 T6J4_19";_4 
chr3_5 galGal3_xenoRefFlat_5 CDS_1 4179277_1 4179338_1 0.000000_5 +_5 0_1 gene_id_5 "T6J4.19;_5 T6J4_19";_5 transcript_id_5 "T6J4.19;_5 T6J4_19";_5 
chr3_6 galGal3_xenoRefFlat_6 exon_1 4179277_2 4179338_2 0.000000_6 +_6 ._1 gene_id_6 "T6J4.19;_6 T6J4_19";_6 transcript_id_6 "T6J4.19;_6 T6J4_19";_6 
chr3_7 galGal3_xenoRefFlat_7 CDS_1 4184594_1 4184751_1 0.000000_7 +_7 0_1 gene_id_7 "T6J4.19;_7 T6J4_19";_7 transcript_id_7 "T6J4.19;_7 T6J4_19";_7 
chr3_8 galGal3_xenoRefFlat_8 exon_1 4184594_2 4184751_2 0.000000_8 +_8 ._1 gene_id_8 "T6J4.19;_8 T6J4_19";_8 transcript_id_8 "T6J4.19;_8 T6J4_19";_8 
chr3_9 galGal3_xenoRefFlat_9 CDS_1 4187403_1 4187538_1 0.000000_9 +_9 1_1 gene_id_9 "T6J4.19;_9 T6J4_19";_9 transcript_id_9 "T6J4.19;_9 T6J4_19";_9 
chr3_10 galGal3_xenoRefFlat_10 exon_1 4187403_2 4187541_1 0.000000_10 +_10 ._1 gene_id_10 "T6J4.19;_10 T6J4_19";_10 transcript_id_10 "T6J4.19;_10 T6J4_19";_10


I am scared that you missed my point. I would like to add the suffix only to the content in inverted commas after gene_id and transcript_id columns.

I hope you got some time to solve my problem. Thanks in advance.

---------- Post updated 06-01-12 at 10:33 AM ---------- Previous update was 05-31-12 at 04:22 PM ----------

Any thoughts friends?
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