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Selected lines from a file based on another file

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# 1  
Old 11-19-2012
Selected lines from a file based on another file
Hello,

I am using Awk in Ubuntu 12.04

First file: I have a file like this:
Code:
SNP1  1  198.2   
SNP2  1  124.5
SNP3  1  124.4
.
.
.

Second file: I have another file like this:
Code:
SNP2
SNP5
SNP10
.
.
.

I want to create a third file like my first file but keeping ONLY the SNPs that exist in the second file using Awk.
For example like an output:
Code:
SNP2 1 124.5
SNP5 1 433.5
SNP10 1 454.2

Thank you very much in advance.
Last edited by Franklin52; 11-19-2012 at 07:55 AM.. Reason: Please use code tags for data and code samples
# 2  
Old 11-19-2012
Try (assuming that the first field will always have numbers):
Code:
awk 'FNR==NR{t=$1;sub($1 FS,"");a[t]=$0;next}{$0=$1 FS a[$1]}1' file1 file2

How big will the first file be?
Last edited by elixir_sinari; 11-19-2012 at 06:37 AM..
# 3  
Old 11-19-2012
It is quite big, it has 441,845 rows and 50 columns.

---------- Post updated at 05:31 AM ---------- Previous update was at 05:17 AM ----------

Thank you so much.

There is a problem, my first file has actually 47 columns, how I can print them all?
# 4  
Old 11-19-2012
You may also try

Code:
awk 'NR==FNR{a[$0]=$0;next}{if(a[$1]){print }}' file2 file1

# 5  
Old 11-19-2012
Check my earlier post.
# 6  
Old 11-19-2012
There seems to be a problem because when I count the number of fields, it gives me 1 field instead of 47. When I check the tail of my dataset, I see there are lines with only the first column.

I want to only keep the SNPs in the first file that exist in the second file.

sorry for asking too many questions.
# 7  
Old 11-19-2012
What about
Code:
$ grep -f file2 file1
SNP2 1 124.5
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