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Full Discussion: Awk: Append new elements to an array
Top Forums Shell Programming and Scripting Awk: Append new elements to an array Post 302897134 by lsantome on Friday 11th of April 2014 07:31:06 AM
Old 04-11-2014
Awk: Append new elements to an array
Hi all,

I'm dealing with a bash script to merge the elements of a set of files and counting how many times each element is present. The last field is the file name.

Sample files:
Code:
head -5 *.tab

==> 3J373_P15Ac1y2_01_LS.tab <==
Code:
chr1    1956362 1956362 G       A       hom     3J373_P15Ac1y2_01_LS.tab
chr1    1957037 1957037 T       C       hom     3J373_P15Ac1y2_01_LS.tab
chr1    1960926 1960926 T       C       hom     3J373_P15Ac1y2_01_LS.tab
chr1    17359676        17359676        C       A       hom     3J373_P15Ac1y2_01_LS.tab
chr1    17371152        17371152        T       C       het     3J373_P15Ac1y2_01_LS.tab

==> 7D300_P15Ac1y2_01_GATK.tab <==
Code:
chr1    1956362 1956362 G       A       het     7D300_P15Ac1y2_01_GATK.tab
chr1    1957037 1957037 T       C       het     7D300_P15Ac1y2_01_GATK.tab
chr1    1959107 1959107 G       C       het     7D300_P15Ac1y2_01_GATK.tab
chr1    1959699 1959699 G       A       het     7D300_P15Ac1y2_01_GATK.tab
chr1    17359676        17359676        C       A       hom     7D300_P15Ac1y2_01_GATK.tab
.
.
.

Up to several dozens of files...

Here is my code:

Code:
cat *.tab \
    | awk 'BEGIN {FS="\t";OFS="\t"} {s[$1":"$2"-"$3";"$4"/"$5]=$0; c[$1":"$2"-"$3";"$4"/"$5]++} END {for (i in s) print i,c[i],$7}' \
    | sort -V \
    > CommonVariants.bed

Output file:
Code:
cat CommonVariants.bed

Code:
chr1:1956362-1956362;G/A    36    7D300_P15Ac1y2_01_LS.tab
chr1:1957037-1957037;T/C    36    7D300_P15Ac1y2_01_LS.tab
chr1:1957112-1957112;C/T    2    7D300_P15Ac1y2_01_LS.tab
chr1:1959107-1959107;G/C    2    7D300_P15Ac1y2_01_LS.tab
chr1:1959138-1959138;G/C    2    7D300_P15Ac1y2_01_LS.tab
chr1:1959549-1959549;G/A    2    7D300_P15Ac1y2_01_LS.tab
chr1:1959699-1959699;G/A    4    7D300_P15Ac1y2_01_LS.tab
chr1:1959789-1959789;A/G    3    7D300_P15Ac1y2_01_LS.tab
chr1:1960674-1960674;C/T    6    7D300_P15Ac1y2_01_LS.tab
chr1:1960926-1960926;T/C    18    7D300_P15Ac1y2_01_LS.tab
chr1:1961144-1961144;C/T    2    7D300_P15Ac1y2_01_LS.tab
chr1:1961408-1961408;C/T    6    7D300_P15Ac1y2_01_LS.tab
chr1:1961466-1961466;C/T    2    7D300_P15Ac1y2_01_LS.tab
chr1:17359676-17359676;C/A    36    7D300_P15Ac1y2_01_LS.tab

I can create the index and count the lines. However I can't figure out how to append the file names into the $7 column.
I guess I have to replace "$7" with an array in the awk statement, but this is too much for me.

I really appreciate any help.

Thank you in advance
Last edited by Scrutinizer; 04-11-2014 at 08:40 AM.. Reason: Additional code tags
 

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