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This will work for any number of columns you have after col #4.

#! /usr/bin/perl -w
use strict;

# Open the input.txt for reading in filehandle FILE
open FILE, "< input.txt";
my $totCols = 0;...

That assertion is unjustified and may fill the OP with unwarranted confidence.

To be clear, I am not suggesting that there is something inherently wrong with Scrutinizer's code. What I am saying...

Without substr:


echo 'Center=128181;Length=461' | nawk -F '=|;' '{ print $2 }'



128181

awk 'match ($0, /=.*;/){print substr($0, RSTART+1, RLENGTH-2)}' file
128181

Factoring out the common string chr:
awk '$1 ~ /^chr(2L|2R|3L|3R|4|X)$/' input | sort -k1,1 -k2,2n
Try to avoid regex's if you can, to improve efficiency. Also, if you happen to know, to a...

I was about to respond to this post to say exactly what you added in your edit. I agree completely.

Shorter isn't always better. That said, the original version can be simplified a little bit:
...

You could do:
awk '$1 ~ /^chr[2-4]*[LRX]*$/' input | sort -k1,1 -k2,2n
EDIT: But If you want to match strictly only chr2L || chr2R || chr3L || chr3R || chr4 || chrX, then above regexp is wrong.
...

Change print "$TF[$i]"; to print "$TF[$i]\t" . rand(1) . "\n";.

With some assumptions:
perl -lane '
@temp=split /[=;]/,$F[1];
for ($i=0;$i<@temp;$i+=2) {
if(not exists $val{$temp[$i] . " " . $F[0]}) {
$val{$temp[$i] . $F[0]}=$temp[$i+1]
}
else {
...

Yeah just corrected the code. Please check now..:)

This is a (very) slight modification to the previous script. You should've mentioned this requirement earlier.
awk 'NR>1{name[NR-1]=$1;for(i=2;i<=NF;i++) if($i==1) { oneset[NR-1,i]=1;count[NR-1]++}}...

awk 'NR>1{name[NR-1]=$1;for(i=2;i<=NF;i++) if($i==1) oneset[NR-1,i]=1}
END{
for(i=1;i<=(NR-1);i++)
{
if(i==1)
{
print "*"
for(j=1;j<=(NR-1);j++)
print name[j]
printf "\n"
}
...

Try
for i in gi*; do echo mv \"$i\" ${i//[|:]/_}; done
The ${i//[|:]/_} is a bash Pattern substitution, so don't expect it to work with other shells.

If happy with the result, remove the echo...

Try this:while read BAM REGION; do samtools view $BAM chrname:$REGION >> $REGION.txt; done <fileremove the region*.txt files before use.

Leave off 'infile' and awk will read from standard input instead.

Try a for loop for the intermediate values, for example:
awk '
p q !=$1 $2{
if(p)print p,q,t,v
t=1
for(i=q+1; i<$2; i++)
printf "- %s 0 -\n", i
p=$1
q=$2
v=$3...

for i in *.bigWig
do
bigWigToBedGraph $i ${i/%bigWig/bedGraph}
done

It is part of printf format string. You can read more about printf here: printf format string - Wikipedia, the free encyclopedia (http://en.wikipedia.org/wiki/Printf)

Single quotes (') are just...

Try: #!/bin/bash
while true;
do
clear;
date |
awk '{print $4}' |
awk -F ":" '{print substr($1,0,1) "\t" substr($1,2,1) "\n" substr($2,0,1) "\t" substr($2,2,1...

You need faToTwoBit compiled in Windows exe (PE) format but against cygwin1.dll not the native windows dll. You can't run native ELF binaries on Cygwin.

As fas as I know, the faToTwoBit...

@@man:
this should help you.
awk '{if($4==8){i=$1+$2;} else{i=$1;} print i"\t"$3"\t"$4}' man.txt | sort -nk 3
Input:

1 100 1 0
5 100 1 8
7 50 1 0
7 ...

$ awk '{print $3,$2,$4}' input.txt | sort | uniq -c | awk '{print $3,$2,$1,$4}' | sort -n
1 10M 1 AAATTTCCGG
5 4M 1 ACGT
5 8M 3 ACCTTGGA
20 12M 3 AACCTTGGCCTT
20 3M 2 TCG

awk 'END {
for (k in c)
print k, c[k], d[k]
}
{
k = $2 OFS $3
c[k]++; d[k] = $NF
}' <filename>

Let us know if the order matters (or just add | sort -nk1 -k2after the script).

awk 'END {
for (k in c)
print k, c[k], d[k]
}
{
k = $2 OFS $3
c[k]++; d[k] = $NF
}' infile

Hard to read here I think since the spacing is off. Here is the
Link (http://www.faqs.org/faqs/unix-faq/shell/shell-differences/)

Shell features

This table below lists most features...