awk to lookup section of file in a range of another file
In the below, I am trying to lookup $1 and $2 from file1, in a range search using $1 $2 $3 of file2. If the search key from file1 is found in file2, then the word low is printed in the last field of that line in the updated file1. Only the last section of file1 needs to be searched, but I am not sure how to do this or if I am on the right track. The last section of file1 is Missing in IDP but found in Reference: and only the lines in this section need to be searched (in this example there are 2 lines). Both files are tab-delimited as well. Thank you .
file1
Code:
Match:
chr15 68521889 C T exonic CLN6 GOOD 50 het 4
chr7 147183143 A G intronic CNTNAP2 GOOD 382 het 22
Missing in Reference but found in IDP:
chr2 51666313 T C intergenic NRXN1,NONE GOOD 108 het 7
chr2 166903445 T C exonic SCN1A GOOD 400 het 28
Missing in IDP but found in Reference:
2 166210776 C T exonic SCN2A c.[2994C>T]+[=] 3095 23.1 24.56
7 148106478 - GT intronic CNTNAP2 c.3716-5_3716-4insGT 4168 28.6 51.01
Match:
chr15 68521889 C T exonic CLN6 GOOD 50 het 4
chr7 147183143 A G intronic CNTNAP2 GOOD 382 het 22
Missing in Reference but found in IDP:
chr2 51666313 T C intergenic NRXN1,NONE GOOD 108 het 7
chr2 166903445 T C exonic SCN1A GOOD 400 het 28
Missing in IDP but found in Reference:
2 166210776 C T exonic SCN2A c.[2994C>T]+[=] 3095 23.1 24.56
7 148106478 - GT intronic CNTNAP2 c.3716-5_3716-4insGT 4168 28.6 51.01 low
I need to get a section of a file based on 2 params. I want the part of the file between param 1 & 2. I have tried a bunch of ways and just can't seem to get it right. Can someone please help me out.....its much appreciated. Here is what I have found that looks like what I want....but doesn't... (12 Replies)
Hi All,
I have two files file1 and file2(lookup file).I need to map more than one keyfields of file1 with file2.how can we achieve it using awk.
file1(max 2.2 million records)
--------------------------
680720|680721|077
680720|680721|978
680721|680722|090
file2(no idea about the... (1 Reply)
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09-10-2016
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