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Oh, thanks, but now, there is another problem, in my actual file, the content of each of the headers is longer than one line, for example:

>ENSGALG00000014675|ENSGALT00000023647|1|1603|1605...

Ok, I added the -F

awk -F "|" 'FNR == NR {a[$1]++} FNR < NR {if ( $1 in a ) print $0}' filetwo fileone

and it works but it only prints the headers and not the content, that is the sequence of...

Hello,

I have a file with such structure:

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

Hello,

I have a data such as this:

ENSGALG00000000189 329 G A 4 2 0
ENSGALG00000000189 518 T C 5 1 0
ENSGALG00000000189 1104 G A 5 1 0
ENSGALG00000000187 3687 G T 5 1 0
ENSGALG00000000187...

Oops, sorry for posting this, I found my mistake:

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

Hello,

I have a file as follows:

ENSGALG00000000189
ENSGALG00000000189
ENSGALG00000000189
ENSGALG00000000215 ...

Hello,

I have a file such as below:

0 0 . . 0 0
0 0 0 0 0 0
1 1 1 1 1 1
1 1 1 1 1 1
0 0 0 1 0 1I want to count...

Hello dear members,

I have one general and one specific question which I will be very grateful if you could help me with them. Let's start with my general question:

1. I am working on cluster...

Hello,

I am puzzled, I am learning awk from the book "effective awk programming".

there is this very simple piece of code in the beginning of the book:
$ awk "BEGIN { print \"Don't Panic!\"...

Hello,

I have a file such as this:
chr1
chr2
chr1
chr2
chr3
chr10
chr4
chr5
chrz
chr1AI want to sort it, I use this command:
sort -k1 -th -n testfilebut I get this output, how can I...

Hello,

I have files as follows:

ACTGCCCTG
ACCGGCTCC
ACAAATTTC
ACCCGGGTTI want to do the following:
I want to find certain strings in each line, for example CT and TT. Then I want the script...

I am using Biopython to process an alignment in fasta format. I need to slice the sequences where there is the first stop codon. So I divided my alignment in codons and found the stop.
I then found...

Hi,

I am using Ubuntu 12.04

I have a file as following:

KHO123
KHO245
KHO456
.
.
.I want to add a second column of characters to my file but I want to write a script to make this...

Hi,

I want to run a script over a series of files with the names :

Sample_1.sorted.bam
Sample_2.sorted.bam
Sample_3.sorted.bam

How can I specify it in my script. Thanks a lot in advance.

Hello,

I have this code to submit a job to cluster in a genomic analysis.

I can't fully understand the first lines of the code:

ref=$1
read1=$2
read1=${read1#*/}
read=${read1%_*_*}
...

Thanks alot for your explanations. I am using Shell in Ubuntu 12.04.
I have already finished the task I needed to do with this script but as I have not written it, I could not understand it well but...

Hi,

I have this piece of code but I can not understand it in details and it is difficult to find in net. What is the function of the $, type, d and prefix here?

This script wants to get each...

Hello,

I have two files as follow:
AFFY_ID RS_ID CHROMOSOME POS_START POS_END ALLELE1 ALLELE2
SNP_A-1780283 rs17011450 chr4 127630275 127630276 C T
SNP_A-1780285 rs6919430 chr6 90919464...

Indeed, but my real file has about 1000 rows and more than 400, 000 columns, I have found this:
{
col2[$1] = col2[$1] $2
col3[$1] = col3[$1] $3
col4[$1] = col4[$1] $4
}

END {

...

Hello,

I have a data format as follows:

Ind1 0 1 2
Ind1 0 2 1
Ind2 1 1 0
Ind2 2 2 0

I want to use AWK to have this output:

Ind1 00 12 21
Ind2 12 12 00

That is to merge each...

Hello,

I have a file as follows:

BTA Pos KLD

4 79.7011 5.7711028907

4 79.6231 5.7083918219

5 20.9112 4.5559494707

5 58.0002 3.4423546273

6 ...

oh yes you are right, thank you very much!

This was so nice of you to correct my code. Thank you very much for it.

Great, thanks a lot!

That works very well, thank you!