Combining loop with awk - for-loop

Question

I need help combining an awk with a loop.
I have two files, one Bedfile.bed and a Samplelist.txt that look like this:
Bedfile.bed
HiC_scaffold_2 1 50001
HiC_scaffold_2 400001 450001
HiC_scaffold_2 800001 850001
Samplelist.txt
sampleA
sampleB
sampleC
I would like to create a new Bedfile for each sample (from the Samplelist.txt) in which I include the sample name as a new column next to each line, and I add the name in the output. Looking like this, e.g., for the first two sample
Bedfile_SampleA.bed
HiC_scaffold_2 1 50001 SampleA
HiC_scaffold_2 400001 450001 SampleA
HiC_scaffold_2 800001 850001 SampleA
Bedfile_SampleB.bed
HiC_scaffold_2 1 50001 SampleB
HiC_scaffold_2 400001 450001 SampleB
HiC_scaffold_2 800001 850001 SampleB
I have done this for one file but I have more than a hundred files, so I would like to do some sort of loop using a sample list.
awk ' {print $1"\t"$2"\t"$3"\t""SampleA"}' Bedfile.bed > Bedfile_SampleA.bed
Any suggestion?

Answer 1

$ awk -v OFS='\t' '
NR==FNR { samples[$0]; next }
FNR == 1 {
base = FILENAME
sub(/\..*/,"",base)
}
{
for ( sample in samples ) {
out = base "_" sample ".bed"
print $0 (NF ? OFS sample : "") > out
}
}
' Samplelist.txt Bedfile.bed
$ head Bedfile_*
==> Bedfile_sampleA.bed <==
HiC_scaffold_2 1 50001 sampleA
HiC_scaffold_2 400001 450001 sampleA
HiC_scaffold_2 800001 850001 sampleA
==> Bedfile_sampleB.bed <==
HiC_scaffold_2 1 50001 sampleB
HiC_scaffold_2 400001 450001 sampleB
HiC_scaffold_2 800001 850001 sampleB
==> Bedfile_sampleC.bed <==
HiC_scaffold_2 1 50001 sampleC
HiC_scaffold_2 400001 450001 sampleC
HiC_scaffold_2 800001 850001 sampleC
The above will work in any awk, assuming you don't have too many output files to exceed the "too many open files" limit. If you do, it'll still work with GNU awk, and there's a simple tweak to make it work with any awk.

Answer 2

Thus is very straightforward in awk. First you read the sample file in memory, and then you process the full bed-file
awk 'BEGIN{OFS="\t"}(FNR==NR){a[$0]; next}{for(i in a){f=FILENAME"."i; print $0,i > f}}' sample.txt bed.txt

Answer 3

You can do the operation and the loop all in AWK, but if you wanted to do the loop 'separately' for another reason, you could use:
while read -r sample
do
awk -v var="$sample" 'BEGIN{OFS="\t"} {print $0, var}' bedfile.bed > bedfile_"$sample".bed
done < samplelist.txt