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Full Discussion: Lookup two values per line (from a second file) and write the smaller value to another file
Top Forums Shell Programming and Scripting Lookup two values per line (from a second file) and write the smaller value to another file Post 302416851 by genehunter on Wednesday 28th of April 2010 01:42:07 AM
Old 04-28-2010
Lookup two values per line (from a second file) and write the smaller value to another file
Hello Unix Gurus,
Please let me know if this is hard to understand and I apologize for my inability to explain better.

I have a file "Foo" with the following structure
Code:
CHR_A         BP_A                         SNP_A  CHR_B         BP_B                         SNP_B           R2
     1      2025239                    rs10910029      1      2025544                    rs10910030     0.997504
     1      2025239                    rs10910029      1      2025659                    rs10752741     0.997504
     1      2025239                    rs10910029      1      2026123                    rs10797413     0.997504
     1      2025239                    rs10910029      1      2030758                     rs4648807     0.905058
     1      2025239                    rs10910029      1      2032403                    rs11584491     0.883846
     1      2025239                    rs10910029      1      2035742                     rs3128337     0.860246
     1      2025239                    rs10910029      1      2037407                     rs3107145     0.844859

I have another file "Bar" with two columns
Code:
SNP       p_value
rs1629826       0.0074785032112008
rs10910030     0.00747871295310032
rs5952098       0.00747983098835803
rs10797413      0.00747988817134826
rs12885929      0.00748196549532576
rs11584491      0.00748416021775555
rs10910029       0.00748489518549456
rs6739969       0.00748668296365185

What I want to accomplish is:
(1) Lookup the p-value of SNP_A and SNP_B in file "Bar" and add these values in adjacent columns to SNP_A and SNP_B

(2) Write the SNP name with the lower p-value per line to another file.

Output would be for (1)
Code:
CHR_A   BP_A	SNP_A  			CHR_B   BP_B      SNP_B           R2			p-SNP_A				p-SNP_B
     1 2025239	rs10910029      1      2025544    rs10910030    0.997504	0.00748489518549456	0.00747871295310032
     1 2025239	rs10910029      1      2025659    rs10752741    0.997504	0.00748489518549456	
     1 2025239	rs10910029      1      2026123    rs10797413    0.997504	0.00748489518549456 0.00747988817134826
     1 2025239	rs10910029      1      2030758    rs4648807     0.905058	0.00748489518549456	
     1 2025239	rs10910029      1      2032403    rs11584491    0.883846	0.00748489518549456	0.00748416021775555
     1 2025239	rs10910029      1      2035742    rs3128337     0.860246	0.00748489518549456	
     1 2025239	rs10910029      1      2037407    rs3107145     0.844859	0.00748489518549456

Output for (2)
Code:
Results.txt
rs10910030	 
rs10910029
rs10797413
rs10910029
rs11584491
rs10910029

Any help is appreciated. I have learned to use a little bit of awk from this site and hence it would be great if the solution is in awk.

Thank you for your time & effort
~GH
Last edited by genehunter; 04-28-2010 at 03:35 AM..
 

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