Search Results

The following seems to do what you want:
awk '
$3 == "gene" || $3 == "protein_coding_gene" {
end = index($NF, ";")
id = ";gene_id=" substr($NF, 4, end - 4)
}
$3 == "exon" {
$0 = $0 id
}...

Is it just a really slow awk script? Or is there hundreds of gigabytes of data? Splitting it in 25 won't speed up a slow disk.

Does it make sense to split up the input data into sections? Is...

Try:LINES=`wc -l Input.file | awk '{print int($1/25)}'`
split -dl$LINES Input.file Input.file
mv Input.file /somewhere/else

for file in Input*; do
./gina.awk $file > out_$file &
done

cat...

sed -e 's/ */\t/1;s/ */\t/1' myFile

Use tr to delete carriage returns:
tr -d '\r' < inputfile > outputfile

Try this:
awk '
FNR == 1 {
c += 1
d = FILENAME
sub ( /\/.*/, X, d )
D[c] = d
}
{
...

Here is an awk approach that might work:
awk '
FNR == 1 {
c += 1
}
{
A[c,FNR] = $5
m = m < FNR ? FNR : m
}
...

Did you check the result1.txt?
Anyways, try this



#!/bin/bash

data[0]=""
key[0]=""
count=0

search_add()
{
inkey=$1;indata=$2;action=$3
if [ $action == ADD ]; then
...

Not very clean though but try this.
You can optimize it to some extend depending on which ever file you think might be bigger.
The highlighted part is what you were asking for, the substring logic....

awk 'ORS=(NF==2)?FS:RS' myFile

$ awk 'NF==2{s=$0;next}NF==1{$0 = s FS $0}1' file

awk -F"\t" -v OFS="\t" 'NF==2 { A=$0 ; getline ; print A,$0 }' inputfile > outputfile

Here is an awk program based on some assumptions:
awk '
NR == FNR {
if ( $0 ~ /\[[A-Z]*\]/ )
D = $0
else
...