Hi Friends,

This is the only solution to my task. So, any help is highly appreciated.

I have a file

Code:

cat input1.bed

chr1 100 200 abc
chr1 120 300 def
chr1 145 226 ghi
chr2 567 600 unix

Now, I have another file by name

Code:

input2.bed (This file is a binary file not readable by the terminal).

But, there is a program in our field that executes by taking this

Code:

input2.bed

Code:

program input_file -chrom -start -end output_file

Now, my task is this

1. Read input1.bed's each record

2. Feed it in the following way to the program, so that the program executes in a continuous loop for each record in input1.bed this way and generate the output files with each input1.bed's record as their name

Code:

program input2.bed -chrom=chr1 -start=100 -end=200 chr1_100_200_op.bed
program input2.bed -chrom=chr1 -start=120 -end=300 chr1_120_300_op.bed
program input2.bed -chrom=chr1 -start=145 -end=226 chr1_145_226_op.bed
program input2.bed -chrom=chr2 -start=567 -end=600 chr2_567_600_op.bed

3. For example, I consider the first output file -

Code:

chr1_100_200_op.bed

.

Code:

cat chr1_100_200_op.bed

chr1 110 120 45.67
chr1 177 189 98.50
chr1 195 200 111.11

4. Now, ignore the first three columns of the above output file, but consider the maximum fourth column value, which is 111.11 and replace the entire contents of my chr1_100_200_op.bed with just the file name, which will be this one

Code:

cat chr1_100_200_op.bed

chr1_100_200 111.11

This is it. Please ask me as many questions as you have for a better solution. Thanks a ton for all your time.