How to match 2 columns where one column has data as a range - extended

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# 1  
Old 09-19-2011
How to match 2 columns where one column has data as a range - extended

Dear all,

there is a nice solution for a text merge where the second file has only variables with a numeric range ( sorry, cannot post URL + thread is closed ). The real world is however more complicated than in the earlier example.

A 1
A 2
A 3
B 1
B 2
B 3
B 4
C 1
C 2
C 3
C 4

file 2
A Gene1 1 2
A Gene2 3 4 
A Gene3 5 6
B Gene4 1 2
C Gene5 3 4

output file required
A 1 Gene1
A 2 Gene1
A 3 Gene2
B 1 Gene4
B 2 Gene4
B 3 -
B 4 -
C 1 -
C 2 -
C 3 Gene5
C 4 Gene5

The earlier code

awk 'NR==FNR{a[$1]=$2;b[$1]=$3;c[$1]=$4;next}
a[$1] && $2 >= b[$1] && $2 <= c[$1]{print $0 FS a[$1];next}
{print $0 FS " -"}' file2 file1

doesn't consider multiple occurrences of A. Can you help with an update?

Last edited by underscore; 09-19-2011 at 07:20 AM.. Reason: mixed code and quote
# 2  
Old 09-19-2011
awk 'NR==FNR{a[$1 FS $3]=$2;b[$1 FS $4]=$2;next}
 {print (a[$0] || b[$0]?$0 FS a[$0] b[$0]:$0 FS "-")}' file2 file1

This User Gave Thanks to malcomex999 For This Post:
# 3  
Old 09-19-2011
thank you

@malcomex999 I am really grateful as my attempts over several hours were unsuccessful. You saved my day :

Last edited by underscore; 09-19-2011 at 09:20 AM.. Reason: typo
# 4  
Old 09-20-2011
Error range not always recognized

Hi - found some errors when running a large dataset. Consider a slightly modified

file 2

A Gene1 1 2
A Gene2 3 4 
A Gene3 5 6
B Gene4 1 5
C Gene5 3 4

Range of Gene4 is not correctly recognized. Can you replicate that?
# 5  
Old 09-22-2011
I think one of main misunderstandings in the approach above is the fact that it doesn't know the address in the associative array. So I am reversing now the input files, combining the best of all worlds and voila

awk 'NR==FNR { a[$2 FS $3]=$2; b[$2 FS $3]=$3; c[$2 FS $3]=$0; next} {for (i=$3;i<=$4;i++) if (c[$1 FS i]) {d[$1 FS i]=$2} } END {for (i in a) print (d[i]?c[i] FS d[i]:c[i] FS " -" ) }' file1 file2

might be a solution. Haven't tested it extensively so far, so be careful.
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