I was wondering whether anyone has any idea what is happening here. I'm using simple code to compare 2 tab delimited files based on column 1 values. If the column1 value of file1 exists in file2, then I'm to print the column4 value in file2 in column3 of file1. Here is my code:



1st I have to produce file1 by concatenating columns 4&5 of the input file:


INPUT FILE:

Code:

1    52828739    rs12044739    C    T
1    52835713    rs72899818    T    C
1    52836736    rs10157619    G    A
1    52844478    rs6684941    A    G

Using this simple code, I reorder columns in the INPUT file and concatenate columns 4 &5:

Code:

awk -F '\t' ' {print $3,$1,$2,$4$5}' OFS="\t" INPUT > file1

This produces the following file1 which looks fine:

Code:

rs12044739    1    52828739    CT
rs72899818    1    52835713    TC
rs10157619    1    52836736    GA
rs6684941    1    52844478    AG

This is file2:

Code:

rs12044739    1    52828739    CC
rs72899818    1    52835713    TC
rs10157619    1    52836736    GG
rs6684941    1    52844478    AA

Using the code:

Code:

awk 'NR == FNR {REP [$1] = $4; next} $1 in REP {$3 = REP[$1]} 1' OFS="\t" file2 file1 > results

Yields the following output file, RESULTS, which so far seems to look fine:

Code:

rs12044739    1    CC    CT
rs72899818    1    TC    TC
rs10157619    1    GG    GA
rs6684941    1    AA    AG

For final processing we need to print all rows for which column3 = column4. So I used this simple code:

Code:

awk -F '\t' '{ if ($3 = $4) print $0}'  OFS="\t" RESULTS > RESULTS2

Thus RESULTS2 should look like this:

Code:

rs72899818    1    TC    TC

Instead what I get is this:

Code:

rs72899818    1    TC    

TC

Any ideas as to what is causing the column4 value to print to the following row?