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Awk: check element in array and it's value


 
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# 1  
Old 11-20-2017
Awk: check element in array and it's value

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:

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

Following code fails:

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

Error:
Code:
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.


Moderator's Comments:
Mod Comment Please use CODE (not QUOTE) tags consistently as required by forum rules!

Last edited by RudiC; 11-20-2017 at 02:56 PM.. Reason: Added / changed CODE tags.
# 2  
Old 11-20-2017
Which of the three lines for chromosome 2 should be selected?
# 3  
Old 11-20-2017
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  
Old 11-20-2017
OK.

For your code, put the && within the single if's parentheses:
Code:
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
Code:
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  
Old 11-20-2017
Code:
 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  
Old 11-20-2017
Use parentheses around the first $4 in arr Right now, you check (!$4) in arr.
# 7  
Old 11-20-2017
I can't get your code working if I change the order.

Code:
 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 Smilie

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