Compare two files and extract info Post: 302935622

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Top Forums Shell Programming and Scripting Compare two files and extract info Post 302935622 by RudiC on Wednesday 18th of February 2015 08:01:32 AM

02-18-2015

Registered User

Any attempts from your side?

---------- Post updated at 13:52 ---------- Previous update was at 13:30 ----------

Anyhow, try

Code:

awk     '!MIN[$6]       {MIN[$6] = 1E100}
         FNR==NR        {CNT[$6]++
                         if ($9 < MIN[$6]) {MIN[$6]=$9; F3[$6]=$3; F7[$6]=$7}
                         next
                        }
         FNR==1         {print $0, " no of SNPs    Top rs ID    Top categ    Top P"
                         next
                        }
                        {$1=$1}
                        {print $0, CNT[$1], F3[$1], F7[$1], MIN[$1]}
        ' file2 OFS="\t" file1
Name    test1    status    P     no of SNPs    Top rs ID    Top categ    Top P
Gene1   0.00236753      1       1.00E-01        6       SNP3    MEDIUM  1.70E-01
Gene2   0.134187        2       2.00E-01        2       SNP7    HIGH    6.34E-01
Gene3   0.000608716     2       3.00E-01        1       SNP9    HIGH    2.94E-01
Gene4   0.0016234       1       4.00E-01        4       SNP12   HIGH    1.55E-01
Gene5   0.000665868     2       5.00E-01        5       SNP15   LOW     2.09E-02

---------- Post updated at 14:01 ---------- Previous update was at 13:52 ----------

This is running into problems as the space in "VERY HIGH" shifts the field count... so the field separator needs to be <TAB>, and both files should comply...replace
' file2 OFS="\t" file1
with
' FS="\t" OFS="\t" file2 file1.

Last edited by RudiC; 02-18-2015 at 09:19 AM..

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