I want to align file1 with file2, first by matching the 3rd, 5th, 7th columns from each file and placing rows in file1 beside the corresponding rows on file2
This is the code I have to keep overlap between the two, but I would like to append file2 with file1. Any help is appreciated!
awk 'NR==FNR {a[$3$5$7];next}($3$5$7 in a){print $0}'
file1
#Scaffold Position Ref. Nuclueotide Pid allele count Pid allele Non-pid allele count Non-pid allele Overlapping gene/region
NW_006532398.1 202035 C 35:0:0:0:0:0 A 0:0:29:0:0:0 C KCND2
NW_006532656.1 289646 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
NW_006532656.1 289656 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
NW_006532656.1 289666 A 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
NW_006532656.1 289676 A 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
NW_006532657.1 636 A 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
NW_006532657.1 646 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
NW_006532657.1 656 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
NW_006532658.1 345 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
file2
#Scaffold Position Ref. Nuclueotide Pid allele count Pid allele Non-pid allele count Non-pid allele
HiC_scaffold_7 49526089 C 0:0:28:0:0:0 A 0:31:0:0:0:0 C
HiC_scaffold_7 49539537 C 27:0:0:0:0:0 T 0:0:0:29:0:0 C
HiC_scaffold_7 49972546 C 20:0:0:0:0:0 T 0:0:0:27:0:0 C
HiC_scaffold_7 49972556 A 20:0:0:0:0:0 T 0:0:0:27:0:0 C
HiC_scaffold_7 49972566 A 20:0:0:0:0:0 T 0:0:0:27:0:0 C
HiC_scaffold_7 49972576 A 20:0:0:0:0:0 T 0:0:0:27:0:0 C
HiC_scaffold_7 49972586 C 20:0:0:0:0:0 T 0:0:0:27:0:0 C
HiC_scaffold_7 49972596 C 20:0:0:0:0:0 T 0:0:0:27:0:0 C
HiC_scaffold_7 49972599 A 20:0:0:0:0:0 A 0:0:0:27:0:0 C
HiC_scaffold_7 49972646 C 20:0:0:0:0:0 T 0:0:0:27:0:0 C
file3
#Scaffold Position Ref. Nuclueotide Pid allele count Pid allele Non-pid allele count Non-pid allele Scaffold Position Ref. Nuclueotide Pid allele count Pid allele Non-pid allele count Non-pid allele
HiC_scaffold_7 49526089 C 0:0:28:0:0:0 A 0:31:0:0:0:0 C NW_006532398.1 202035 C 35:0:0:0:0:0 A 0:0:29:0:0:0 C KCND2
HiC_scaffold_7 49539537 C 27:0:0:0:0:0 T 0:0:0:29:0:0 C NW_006532656.1 289646 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
HiC_scaffold_7 49972546 C 20:0:0:0:0:0 T 0:0:0:27:0:0 C NW_006532656.1 289656 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
HiC_scaffold_7 49972556 A 20:0:0:0:0:0 T 0:0:0:27:0:0 C NW_006532656.1 289666 A 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
HiC_scaffold_7 49972566 A 20:0:0:0:0:0 T 0:0:0:27:0:0 C NW_006532656.1 289676 A 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
HiC_scaffold_7 49972576 A 20:0:0:0:0:0 T 0:0:0:27:0:0 C NW_006532657.1 636 A 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
HiC_scaffold_7 49972586 C 20:0:0:0:0:0 T 0:0:0:27:0:0 C NW_006532657.1 646 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
HiC_scaffold_7 49972596 C 20:0:0:0:0:0 T 0:0:0:27:0:0 C NW_006532657.1 656 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1
HiC_scaffold_7 49972599 A 20:0:0:0:0:0 A 0:0:0:27:0:0 C
HiC_scaffold_7 49972646 C 20:0:0:0:0:0 T 0:0:0:27:0:0 C NW_006532658.1 345 C 0:26:0:0:0:0 T 0:0:26:0:0:0 C CNTN1