Thanks for the responses.

Unfortunately, upon looking closer at your example input files, there are no entries in f1 where both endpoints of any line in f2 fall within the ranges specified in f1. In the last line of f2 $2 falls inside the range specified in the first line in f1 but $3 does not.

And, despite what you said about the input files being tab delimited, the samples you provided don't contain any <tab> characters. And, since you said that the real files you're using do contain some <space>s between field 3 and 4 and after field4, the following code assumes that strings of one or more <space> and/or <tab> characters separate field and that any <space> and <tab> characters after field 4 are to be ignored. (As written, the code shown below will not work if a line in either input file contains any leading <space> or <tab> characters.)

So, given the above and assuming that you just want there to be some overlap between the ranges specified in a line in f1 and in a line in f2, maybe the following will do what you want:

Code:

#!/bin/ksh
awk '
BEGIN{	FS = "[[:blank:]]+|_"
	OFS = "\t"
}
FNR == NR {
	# Note that this code assumes that the min and max ranges in the first
	# input file are presented with the minimum values arranged in
	# increasing order for each $1, $NF set of values.
	max[$1, $4, ++count[$1, $4]] = $3	# Save max value with count of
						# lines with the same $1 and $4
						# value from the first input
						# file.
	min[$1, $4, count[$1, $4]] = $2		# Save corresponding min value.
	next					# Skip to next input line.
}
{	for(i = 1; i <= count[$1, $4]; i++) {
		# If the minimum value on this line is greater than the saved
		# maximum value we are looking at now or the maximum value on
		# this line is less than thee save minimum value we are looking
		# at now, there cannot be a matching entry for this $1,$4 value
		# pair.
		if($2 > max[$1, $4, i] || $3 < min[$1, $4, i])
			break
		# If the minimum or maximum on this line is within range, we
		# have found what we are looking for.
		if(($2 >= min[$1, $4, i]) || $3 <= max[$1, $4, i]) {
			print $1, $4, min[$1, $4, i], max[$1, $4, i], "exon"
			next
		}
	}

	# No entry was found for this $1,$4 value pair.  Report "intron" found.
	print $0, "intron"
}' "${1:-f1}" f2

This uses <tab> as the output field separator, but on output lines that end in "intron", <space>s in the input will not be converted to <tab>s in the output.

If you run the above script with no operands (or with the operand f1 or with the operand f) from your sample input files, it will produce the output:

Code:

chr7    94024333    94024423    COL1A2_cds_0_0_chr7_94024344_f  0   +	intron
chr7    94027049    94027080    COL1A2_cds_1_0_chr7_94027060_f  0   +	intron
chr7	COL1A2	94027591	94027701	exon

Note that the above code does not set SUBSEP since it was not used in your script and isn't needed in the code shown above. Note also that the field separator I'm using the code above uses any sequence of one or more <space>s and/or <tab>s to treated as a field separator and uses every <underscore> as a field separator. That means that the subfields you were splitting into the array named array in your code will all be treated as separate fields in the code above. (That means I don't have to call split() to break that string into subfields.)

The sample files you provided to test any of the "corner" cases where I might have missed something. I think it will work OK, but I haven't performed enough extensive testing to give you any kind of guarantee.

Hope this helps,
Don