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Hi bakunin,
It will with a recent ksh (such as version 93u+). It might with a recent bash, but not with bash version 3.26 (the version included with the latest macOS release) where the following...

What you have looks like it would try to change a file named FILE_1000G.vcf to instead have the literal name $filename_1000G.vcf assuming that the only file in the directory where you run this script...

Are you sure you have the code as posted? The solution I presented shouldn't be able to print more lines than is in file2. I suspect you don't have and END { block and the for loop is executing for...

If vgersh99's solution if matching lines are less than 30 lines apart some lines are printed multiple times (overlapping regions).

Try this modification:

BEGIN {
if(!ba) ba=2
}
FNR == NR {...

something along these lines:
default 2 lines before/after
awk -f gene.awk file2.txt file1.txt
or 30 lines before/after
awk -v ba=30 -f gene.awk file2.txt file1.txt
where gene.awk is:

BEGIN...

I note that none of the data you posted looks like it came from strictly tab-separated files. I suspect rogue spaces and/or carriage returns in your data.

From your example file1 and file2 I get...

How about, hoping that any invisible surprises like the ones corona688 mentioned will have been taken care of, and untested, from a windows machine, so bear with me:


awk -F "\t" 'NR == FNR...

What Rudi & Corona are saying: UNIX text files have different carriage control characters from windows text files - like tab delimited Excel output.

cleanup windows files == dos2unix command:
...

awk -F '\t' '
# when FNR==NR (only true for the FIRST file on cli),
# populate array f3 indexed by $1 (first field) in the file (file3)
# next - advance to the next input record/line in file3...

awk -F '\t' 'FNR==NR {f3[$1];next} $1 in f3' OFS="\t" file3 file1.txt > file2.txt

please provide the output of cat -vet file1.txt using code tags.
With the properly formatted file1.txt (tab-delimited fields), I get:

awk -F '\t' 'FNR==NR {f3[$1];next} $1 in f3' OFS="\t"...

Would
awk 'NR == FNR {REP[$1,$4] = $2; next} ($1,$4) in REP {$2 = REP[$1,$4]; CNT++} 1; END {print CNT}' OFS="\t" file2 file1do what you need?

Hello Geneanalyst,

If your Input_file is same as shown samples then following may help you on same.

awk 'FNR==NR&&FNR>1{a[$1]=$NF;next} FNR>1{if(a[$1]){$NF=$(NF-1)=""} else {$(NF-1)=OFS $(NF-1)...

Try
awk 'NR == FNR {REP[$1] = $4; next} $1 in REP && FNR > 1 {$4 = substr (REP[$1], 1, 1); $5 = substr ( REP[$1], 2, 2); CNT++} 1; END {print CNT}' OFS="\t" file2 file1

Hello Geneanalys,

Could you please try following and let me know if this helps you. (tested with GNU awk)

awk 'FNR==NR{num=split($NF,array,"");for(i=1;i<=num;i++){val=val?val OFS...

Try
awk 'NR == FNR {REP[$1] = $4; next} $1 in REP && FNR > 1 {$4 = substr (REP[$1], 1, 1); $5 = substr ( REP[$1], 2, 1)} 1' OFS="\t" file2 file1
rsid chromosome position allele1 allele2...

Hi, try:
awk '
NR==1 {
next
}

NR==FNR {
A[$1]=substr($4,1,1)
B[$1]=substr($4,2)
next
}

$1 in A {
$4=A[$1]
$5=B[$1]
}
1
' OFS='\t' IN2 IN1

Hi.

I like awk solutions. However, I also like packaged solutions. In this case GNU datamash can do the grouping and summing with:
datamash -g 1 sum 2,3
which will sum fields 2 and 3 for items...

Here is a copy of RudiC's code with comments added describing what each section of code is doing:
awk ' # Invoke awk and start script to be run by awk.
BEGIN {# Before any lines are read from any...

Try also
awk '
BEGIN {FMT = "%-13s%-17s%-17s\n"
printf FMT, "SAMPLE", "TOTAL DERIVED", "TOTAL ANCESTRAL"
}
FNR > 1 {SEQ[FNR] = $1
SUMD[$1] += $2
SUMA[$1]...

Hi, try:
awk '{split($0,F)} getline<f>0 && NR>1{$2+=F[2]; $3+=F[3]}1' f=array1 array2

Or you could try an approach like this which should work with 2 or more arrays:
awk '
FNR==1 {
...

Hello Geneanalyst,

Could you please try following and let me know if this helps you.


awk 'BEGIN{print "SAMPLE TOTAL DERIVED TOTAL ANCESTRAL"} FNR==NR{a[$1]=$2;b[$1]=$3;next}...

Based on your sample, where there is NO other field containing "a","c","g", or "t", this could work:
sed 'y/acgt/ACGT/' file

awk '
{
if (str ~ ":" $6 ":") $6=toupper($6);
print $0;
}' str=":a:c:g:t:" datafile
or
awk '$6=toupper($6)' datafile

Note that = is an assignment operator. It assigns the value of right side expression to left side.

But == is an equal to operator. It compares the value of both sides. Hence you have to use == in...