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Thanks for the correction. And there is yet another bug.
Hopefully fixed now:
sort Input.txt | uniq -c | sort -k2,2 -k1,1rn | awk '{ if ($2!=p2 || $1==p1) {print $2,$3,$1; p1=$1} else {p1=""}}...

A single awk command could do this more efficiently, but I find the logic easier to express with a couple of sort commands, one uniq command, and a read loop in the shell...
#!/bin/ksh
last_gene=""...

Hi, another one to get you started:

The code needs to modified still to print the highest number of connections rather than only the number of connections...

awk's associative arrays are nice...

What have you tried so far?

---------- Post updated at 05:24 ---------- Previous update was at 04:06 ----------

Funny, i just looked at the output (ignoring the BP8 as i see now - sorry), and...

This post (https://www.unix.com/302738343-post7.html) results (after adapting the output format) in CPLX9PC-4943 CpxID123 CpxID126 CPLX9PC-5763 CpxID13 CPLX9PC-6163...

Or..

$ awk '{A[$1,$2]=$3;B[$1]++;C[$2]++}END{for(i in C){s=s?s"\t"i:"\t"i}
print s;
for(i in B){s=i;
for(j in C){s=s"\t"A[j,i]}
print s}}' file

a b c
a 1 2 ...

If you don't have GNU R and want a table that adjusts to the input given, you could try something like:
awk '
NF == 3 {
if(!($1 in rh)) {
# Add a new row heading.
...

Try this:
awk '
{a[$1,$2]=$3; b[$1];}
END{
for(i in b) #print header
printf("\t%s",i);
printf("\n");
for(i in b) { #each row
printf("%s\t",i);
for(j in b) #each...

How about this ?

#!/usr/bin/perl
use strict;
my $file1=shift;
my $file2=shift;
my %seen;
open (FH,"$file1") or die "can not open file $file1 - $! \n";
while (<FH>) {
chomp;
...

For your first request, you might want to give this a shot:awk 'NR==1 {Pat = "["}
NR==FNR {Pat = Pat $1;next}
FNR==1 {Pat=Pat"]"}
{for (i=1;...

awk ' BEGIN {
c = 1
} FNR == NR {
A[$0] = $0
next
} {
M_F = "C" c "match.txt"
N_F = "C" c "non_match.txt"

for ( j = 1; j <= NF; j++ )
...

Perhaps there are tabs present in the input file?
awk -F'[, \t]' ...

This works for me (using gawk):
gawk -F',| ' '!(a[$1,$2]++ + a[$2,$1]++)'

Try:
awk '{ split($1, f, /,/)
if((f[2]","f[1]) in o) next
o[$1]
print
}' input
As always, if you are using a Solaris/SunOS system, use /usr/xpg4/bin/awk or nawk instead...

Whenever you have sed | awk | grep | kitchen | sink, it can probably be done all in one awk. It's a lot more than a glorified 'cut'.

1) Search for a line containing CYTOCHROME C where there's two...

I'm not sure about everything you want to do, but I think this does most of it:

sed -n '/^[\ \t]*COMPND.*CYTOCHROME\ C.*/{n;p;}' out.test | awk -F":" '{print $2}' | sed 's/[\ \,]//g'

sed -...

awk 'NR==FNR{a[$1]=$2;next}{print $1,a[$1]}' small_file.txt huge_file.txt

$ cat huge_file.txt
a
a
ab
b
hh
$ cat small_file.txt
a 1.5
b 2.5
ab 7.5
cd 1.1
$ awk 'NR==FNR{buff[$1]=$0;next} {if(buff[$1]!="") print buff[$1]}' small_file.txt huge_file.txt
a 1.5
a...