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NR==FNR confusions

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# 1  
Old 08-15-2012
NR==FNR confusions
This has been asked and answered hundreds of times, but I can't understand the syntax of awk's NR==FNR trick for merging files and printing the correct columns.

Here's my File 1

Code:
   1   rs8179466     224176    A        ADD     1037      1.066   0.1421   0.8065    1.408       0.4468        0.655
   1   rs3094315     742429    G        ADD     1103     0.8797   0.1553   0.6488    1.193      -0.8254       0.4091
   1   rs3115860     743268    C        ADD     1092     0.9057   0.1663   0.6538    1.255      -0.5958       0.5513
   1   rs3131968     744055    A        ADD       92      1.204   0.6454   0.3398    4.266       0.2876       0.7737
   1   rs3131967     744197    A        ADD     1088     0.8947   0.1705   0.6406     1.25      -0.6524       0.5141

Here's my File 2
Code:
1	rs8179466	0	224176	A	G
1	rs6594028	0	554461	0	G
1	rs10458597	0	554484	0	C
1	rs9701055	0	555296	0	C
1	rs9699599	0	558185	0	A
1	rs3094315	0	742429	G	A
1	rs3115860	0	743268	C	A
1	rs3131968	0	744055	A	G
1	rs3131967	0	744197	A	G
1	rs3115850	0	751010	A	G
1	rs2519016	0	755811	0	T

Final output should look like:

Code:
   1   rs8179466     224176    A        ADD     1037      1.066   0.1421   0.8065    1.408       0.4468        0.655   G
   1   rs3094315     742429    G        ADD     1103     0.8797   0.1553   0.6488    1.193      -0.8254       0.4091   A
   1   rs3115860     743268    C        ADD     1092     0.9057   0.1663   0.6538    1.255      -0.5958       0.5513  A
   1   rs3131968     744055    A        ADD       92      1.204   0.6454   0.3398    4.266       0.2876       0.7737  G
   1   rs3131967     744197    A        ADD     1088     0.8947   0.1705   0.6406     1.25      -0.6524       0.5141  G

In essence, having matched via the second column in File 1, I want to append the fifth column from File 2, as a new 13th column, and output to File 3. Thanks for pointers.


Moderator's Comments:
Mod Comment Please use code tags next time for your code and data. Using table tags instead makes it really hard to read, thanks.
Last edited by zaxxon; 08-15-2012 at 08:53 AM.. Reason: table tags to code tags
# 2  
Old 08-15-2012
Code:
awk 'NR==FNR{_[$2]=$0; next} _[$2] {print _[$2] "\t" $6}' f1 f2

NR has Number of the Record combined for all files given as input (16 Records). FNR just the Number of Records for the current file.

NR==FNR works like this:
Code:
$ awk '{print "NR:", NR " FNR:", FNR}' f1 f2
NR: 1 FNR: 1             <---- here starts f1
NR: 2 FNR: 2
NR: 3 FNR: 3
NR: 4 FNR: 4
NR: 5 FNR: 5
NR: 6 FNR: 1             <---- here starts f2
NR: 7 FNR: 2
NR: 8 FNR: 3
NR: 9 FNR: 4
NR: 10 FNR: 5
NR: 11 FNR: 6
NR: 12 FNR: 7
NR: 13 FNR: 8
NR: 14 FNR: 9
NR: 15 FNR: 10
NR: 16 FNR: 11

So when NR and FNR are not equal anymore, we must be in the second file f2. The next just helps, that the next following statement is not executed and so we just read in f1 into an associative array for later use, when we are in f2, (ie. when NR==FNR) is not true anymore.
Last edited by zaxxon; 08-15-2012 at 09:27 AM.. Reason: typo
# 3  
Old 08-15-2012
Code:
awk 'NR==FNR{a[$2]=$6;next} {for(x in a){if($2==x){print $0,a[x]}}}' file2 file1

# 4  
Old 08-15-2012
Perfect! Thank you both. Much clearer now.
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