awk setting variables to make a range - variables

Question

I have the following two files:
File 1:
1 290 rs1345
2 450 rs5313
1 1120 rs4523
2 790 rs4325
File 2:
1 201 LDLR
2 714 APOA5
1 818 NOTCH5
1 514 TTN
I wish to isolate only the rows in file 2 in which the second field is within 100 units of the second field in file 1 (if field 1 matches):
Desired output: (note the third field is from the matching line in file1).
1 201 LDLR rs1345
2 714 APOA5 rs4325
I tried using the following code:
for i in {1..4} #there are 4 lines in file2
do
chr=$(awk 'NR=="'${i}'" { print $1 }' file2)
pos=$(awk 'NR=="'${i}'" { print $2 }' file2)
gene=$(awk 'NR=="'${i}'" { print $3 }' file2)
start=$(echo $pos | awk '{print $1-100}') #start and end variables for 100 unit range
end=$(echo $pos | awk '{print $1+100}')
awk '{if ($1=="'$chr'" && $2 > "'$start'" && $2 < "'$end'") print "'$chr'","'$pos'","'$gene'"$3}' file1
done
The code is not working, I believe something is wrong with my start and end variables, because when I echo $start, I get 414, which doesn't make sense to me and I get 614 when i echo $end.
I understand this question might be difficult to understand so please ask me if any clarification is necessary.
Thank you.

Answer 1

The difficulty is that $1 is not a unique key, so some care needs to be taken with the data structure to store the data in file 1.
With GNU awk, you can use arrays of arrays:
gawk '
NR==FNR {f1[$1][$2] = $3; next}
$1 in f1 {
for (val in f1[$1])
if (val-100 <= $2 && $2 <= val+100)
print $0, f1[$1][val]
}
' file1 file2
Otherwise, you have to use a one-dimensional array and stuff 2 pieces of information into the key:
awk '
NR==FNR {f1[$1,$2] = $3; next}
{
for (key in f1) {
split(key, a, SUBSEP)
if (a[1] == $1 && a[2]-100 <= $2 && $2 <= a[2]+100)
print $0, f1[key]
}
}
' file1 file2
That works with mawk and nawk (and gawk)

Answer 2

#!/usr/bin/python
import pandas as pd
from StringIO import StringIO
file1 = """
1 290 rs1345
2 450 rs5313
1 1120 rs4523
2 790 rs4325
"""
file2 = """
1 201 LDLR
2 714 APOA5
1 818 NOTCH5
1 514 TTN
"""
sio = StringIO(file1)
df1 = pd.read_table(sio, sep=" ", header=None)
df1.columns = ["a", "b", "c"]
sio = StringIO(file2)
df2 = pd.read_table(sio, sep=" ", header=None)
df2.columns = ["a", "b", "c"]
df = pd.merge(df2, df1, left_on="a", right_on="a", how="outer")
#query is intuitive
r = df.query("b_y-100 < b_x <b_y + 100")
print r[["a", "b_x", "c_x", "c_y"]]
output:
a b_x c_x c_y
0 1 201 LDLR rs1345
7 2 714 APOA5 rs4325
pandas is the right tool to do such tabular data manipulation.