How to get values from one file that fall in a list of ranges from another file - bash

Question

I have bunch of files with sorted numerical values, in example:
cat tag_1_file.val
234
551
626
cat tag_2_file.val
12
1023
1099
etc.
And one file with tags and value ranges that fit my needs. Values are sorted first by tag, then by 2nd column, then by 3rd. Ranges may overlap.
cat ranges.val
tag_1 200 300
tag_1 600 635
tag_2 421 443
and so on.
So I try to loop through file with ranges and then look for all values that fall in range (in every line) in file with appropriate tag:
cat ~/blahblah/ranges.val | while read -a line;
#read line as array
do
cat ~/blahblah/${line[0]}_file.val | while read number;
#get tag name and cat the appropriate file
do
if [[ "$number" -ge "${line[1]}" ]] && [[ "$number" -le "${line[2]}" ]]
#check if current value fall into range
then
echo $number >> ${line[0]}.output
#toss the value that fall into interval to another file
elif [[ "$number" -gt "${line[2]}" ]]
then break
fi
done
done
But these two nested while loops are deadly slow with huge files containing 100M+ lines.
I think, there must be more efficient way of doing such things and I'd be grateful for any hint.
UPD: The expected output based on this example is:
cat file tag_1.output
234
626

Answer 1

Have you tried recoding the inner loop in something more efficient than Bash? Perl would probably be good enough:
while read tag low hi; do
perl -nle "print if \$_ >= ${low} && \$_ <= ${hi}" \
<${tag}_file.val >>${tag}.output
done <ranges.val
The behaviour if this version is slightly different in two ways - the loop doesn't bail out once the high point is reached, and the output file is created even if it is empty. Over to you if that isn't what you want!

Answer 2

another not so efficient implementation with awk
$ awk 'NR==FNR {t[NR]=$1; s[NR]=$2; e[NR]=$3; next}
{for(k in t)
if(t[k]==FILENAME) {
inout = t[k] "." ((s[k]<=$1 && $1<=e[k])?"in":"out");
print > inout;
next}}' ranges tag_1 tag_2
$ head tag_?.*
==> tag_1.in <==
234
==> tag_1.out <==
551
626
==> tag_2.out <==
12
1023
1099
note that I renamed files to match the tag names, otherwise you have to add tag extraction from filenames. Suffix ".in" for in ranges and ".out" for not. Depends on the sorted order of the files. If you have thousands of tag files adding a another layer to filter out the ranges per tag will speed it up. Now it iterates over ranges.

Answer 3

I'd write
while read -u3 -r tag start end; do
f="${tag}_file.val"
if [[ -r $f ]]; then
while read -u4 -r num; do
(( start <= num && num <= end )) && echo "$num"
done 4< "$f"
fi
done 3< ranges.val
I'm deliberately reading the files on separate file descriptors, otherwise the inner while-read loop will also slurp up the rest of "ranges.val".
bash while-read loops are very slow. I'll be back if a few minutes with an alternate solution
here's a GNU awk answer (requires, I believe, a fairly recent version)
gawk '
#load "filefuncs"
function read_file(tag, start, end, file, number, statdata) {
file = tag "_file.val"
if (stat(file, statdata) != -1) {
while (getline number < file) {
if (start <= number && number <= end) print number
}
}
}
{read_file($1, $2, $3)}
' ranges.val
perl
perl -Mautodie -ane '
$file = $F[0] . "_file.val";
next unless -r $file;
open $fh, "<", $file;
while ($num = <$fh>) {
print $num if $F[1] <= $num and $num <= $F[2]
}
close $fh;
' ranges.val

Answer 4

I have a solution for you from bioinformatics:
We have a format and a tool for this kind of task.
The format called .bed is used for description of ranges on chromosomes, but should work with your tags too.
The best toolset for this format is bedtools, which is lightning fast.
The specific tool, which might help you is intersect.
With this installed it becomes a task of formating the data for the tool:
#!/bin/bash
#reformating your positions to .bed format;
#1 adding the tag to each line
#2 repeating the position to make it a range
#3 converting to tab-separation
awk -F $'\t' 'BEGIN {OFS = FS} {print FILENAME, $0, $0}' *_file.val | sed 's/_file.val//g' >all_positions_in_one_range_file.bed
#making your range-file tab-separated
sed 's/ /\t/g' ranges.val >ranges_with_tab.bed
#doing the real comparision of the ranges with bedtools
bedtools intersect -a all_positions_in_one-range_file.bed -b ranges_with_tab.bed >all_positions_intersected.bed
#spliting the one result file back into files named by your tag
awk -F $'\t' '{print $2 >$1".out"}' all_positions_intersected.bed
Or if you prefer oneliners:
bedtools intersect -a <(awk -F $'\t' 'BEGIN {OFS = FS} {print FILENAME, $0, $0}' *_file.val | sed 's/_file.val//g') -b <(sed 's/ /\t/g' ranges.val) | awk -F $'\t' '{print $2 >$1".out"}'