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$ cat file1
>ENSGALG00000000011|ENSGALT00000000012|57|1123|1125
AACTGTGTGTTTTTT
>ENSGALG00000000012|ENSGALT00000000013|57|1145|1155
AAAAAAGGTCCTGTGTGC...

i think you can give a try with awk -F option to specify the filed limiter of your choice.

Try:awk '{a[$1]+=$6}END{for (i in a) print i,a[i]}' file

Try:
awk '{count[$1]++} END{for (genes in count) print genes, count[genes]}' ZGenes

Waaay to complicated! Tryawk '{CNT[0]=CNT[1]=0; for (i=1; i<=NF; i++) CNT[$i]++; print CNT[0], CNT[1]}' file
4 0
6 0
0 6
0 6
4 2

What shell are you using?

I'm a bit confused with what it is trying to do, but here goes:-

for i in $(find /file directory/ -type d | grep file name)
do
prefix=`echo $i | cut -f5 -d"/"`...

-type d means only find directories.
Go to a directory tree and experiment:


$ find . -type f -print
$ find . -type d -print
prefix is a variable here. It's holds a value.
For example, if the...

find /file directory/ -type d => list out all the directories (-type d) in /file directory/
grep file_name => finds the file_name from the list
$(command) => pretend the result of the command to...

In general, for an efficient merge operation, you need to have two files.
If you have one file, the shell can open it twice with another file descriptor.

#!/bin/sh
sort -k4,4 infile |
(
# in...

The code provided by in2nix4life is much better, but here is a corrected version of what Homa was trying to do:
awk -F ' ' -v OFS=' ' 'FNR == NR { o[$1] = NR;next }
{ $1 = o[$1]" "$1;print }' File1...

A moment, that doesn't look quite right.

[edit] I was restoring four columns when I only needed three. Remove the $4=D from the code and it works.

$ awk 'NR==FNR { ARR[$4]=$0 ; next }; $1 in ARR { A=$1 ; B=$2; C=$3; D=$4 ; $0=ARR[$1]; $1=A; $2=B; $3=C } 1' datafile datafile

F0100010 A C F0100010 A C BTA-29644-no-rs 7.29827
F0100020 A G...

Oh, I see. You don't want it sorted. You want columns 4 through n of all rows moved such that column 1 lines up with column 4.

Working on it.

awk 'FNR==NR{a[$1]=$0} NR>FNR && ($1 in a) {print a[$1]}' file2 file1 > file3

I think you have edited your previous input....:D

As per your previous input i have considered as you want only first digit of $8.

That's why i used substr()

substr($8,1,1) - Prints only...

Assuming your file structure as it is.

Try....

awk '{ $1=$1+$7+$(NF-1);$2=$2+substr($8,1,1)+$NF;$7=$8="";gsub(" +"," ",$0);NF-=2;}1' file

If your all file1 entries are present in file2 then my script will produce correct output as what you need.

Try

awk 'NR==FNR{X[$1]=$2" "$3;next}{if(X[$2]){split(X[$2],P," ")
if(P[1] == P[2]){if($3 != $4){print $2,$3,$4;delete X[$2]}}else{print $2,X[$2];delete X[$2]}}}' file1 file2

Try:awk 'NR==FNR&&$3!=$4{a[$2]=$3" "$4}NR==FNR{next}$1 in a{$2=a[$1];$3="";}1' file2 file1

Hi Mr complex,

could you please let me know how it works ?


awk '!a[$1]++' infile

awk '!a[$1]++' infile

There was a typo in my previous comment, you need to add option -n (for numeric sort)

Cheers ;)

Just use paste as first suggested by bipinajith. It was created for this specific task.

Memory consumption shouldn't be an issue since paste doesn't need to read more than one line at a time to do...

Alternative awk:
awk '{getline $(NF+1)<f}1' f=file2 file1

I'm not sure about the memory utilization. If you insist a solution using awk here it is:-

awk 'NR==FNR{a[FNR]=$0;next} {print a[FNR], $0 } ' file1 file2