Awk: check element in array and it's value

Shell Programming and Scripting
1

Hello,
I want to see if element exists in array, if so then, check it's corresponding value.

Column 4 is position and column 1 is the chromosome for it. There are duplicates for one position on one chromosome.

I want to check if same position exists on different chromosome:

Data format:

2       rs267607987     0       47702411        0       T
2       seq-rs587779123 0       47702411        0       I
2       seq-rs587779124 0       47702411        0       D
11      seq-rs730880711 0       47364479        0       I
11      seq-rs863225110 0       47364479        0       I
11      seq-rs863225271 0       47364479        0       I
11      seq-rs397515973 0       47359006        0       D
11      seq-rs727503187 0       47359006        0       D
11      seq-rs730880654 0       47359006        0       D
17      DUP-rs80358150  0       41209068        0       C
17      rs273901754     0       41209068        0       D
17      rs80358150      0       41209068        0       C
17       seq-rs5827779124 0       47702411        0       D

I want to check if position column 4 has duplicates on different values for column 1.
in this case:

2       seq-rs587779124 0       47702411        0       D
17       seq-rs5827779124 0       47702411        0       D

Following code fails:

awk ' {if ($4 in arr) && if (arr[$4]==$1){ print arr[$4],$4} else {arr[$4]=$1} }' testcol.txt

Error:

awk:  {if ($4 in arr) && if (arr[$4]==$1){ print arr[$4],$4} else {arr[$4]=$1} }
awk:                  ^ syntax error

Would really appreciate any guidance here.

2

Which of the three lines for chromosome 2 should be selected?

3

It's not important which of the three lines are to be selected from chromosome 2. I'd like to see if same position is present across different chrosomes.

4

OK.

For your code, put the && within the single if 's parentheses:

awk ' {if (($4 in arr) && (arr[$4]==$1)) { print arr[$4],$4} else {arr[$4]=$1} }' file

But this won't print your desired result. Try

awk '($4 in LN) && ($1 != CHR[$4]) {print LN[$4]; print} {LN[$4] = $0; CHR[$4] = $1}' file
2       seq-rs587779124 0       47702411        0       D
17       seq-rs5827779124 0       47702411        0       D
5 
 awk ' {if (! $4 in arr){arr[$4]=$1} if ( ($4 in arr) && (arr[$4]!=$1 ) ){print "Isseu "} }' testcol.txt

I got the && working but the condition fails. Can't figure out why. I can copy paste your code, but would like to know bug in mine.

6

Use parentheses around the first $4 in arr Right now, you check (!$4) in arr .

7

I can't get your code working if I change the order.

 awk ' {if (! $4 in CHR){ CHR[$4]=$1; LN[$4]=$0 } { if ( ($4 in LN) && (CHR[$4] != $1 ) ){print } } }' testcol.txt

I'm totally lost what's wrong :frowning:

8

Hi, try:

(!($4 in CHR))

rather than

(! $4 in CHR)
9

Got it. Thank you. :slight_smile: