Sorry if this is a super simple issue, but am extremely new to this and am trying to teach myself as I go along. But can someone please help me out?
I have a data file similar to this for many samples, for all chromosomes
I would like to determine the maximum and minimum bp for each chromosome for each sample, and then output the distance between the min and max bp for each chromosome for each sample.
As I am super new to all this, and I have noone to help me, I was wondering if someone here could help me out?
I have so far written this:
And I keep getting the thi following syntax error message
I have no idea what it means - please help? Any advice would be greatly appreciated.
Best
V
Last edited by Franklin52; 08-18-2014 at 11:08 AM..
Reason: Please use code tags
I am writing a shell script that simulates the `wc -w` command without actually using wc itself. My problem is that the script will only read the first line of the file and just keep looping through it. I have tried both while and for loops and got the same result. Can anyone help?
... (1 Reply)
Good morning,
Sir's i would like to ask for help regarding to my awk and loop problem, a script that will check my files a and b then if it will see there was a time below 3am it will echo the file that contains below 3am file, for this example it will redirect the file a to an output.
$ cat a... (3 Replies)
i have a script that will read each line and then grep a particular pattern and do some_stuff. Below the script
while read j
do
q1=0
q1=`$j | grep 'INFO - LPBatch:' | wc -l`
if
then
$j | tr -s " " | cut -d " " -f8,42,43 >> nav1.txt
fi
q2=0
q2=`$j | grep 'INFO - Number of Intervals... (12 Replies)
Hi All,
How to read a file upto last line(End Of Line)
I wrote below program:
cat R2_20060719.610.txt | while read LINE
do
echo "$LINE"
done
above code reading all lines from a file and skipping last line......
is there anything wrong in my code.
Please help me out from this... (20 Replies)
Hi all,
i write a script c shell
set i = 1
while ( $i <= $#array )
echo "$array"
@ i++
end
i want to set it to i = i +2 in that statement . Can anybody help me?
---------- Post updated at 02:46 PM ---------- Previous update was at 02:35 PM ----------
anybody not how to solve it??? (2 Replies)
Hello forum memebers.
can you correct the simple while program.
#! /bin/ksh
count=10
while
do
echo $count
count='expr$count-1'
done
I think it will print 10 to 1 numbers but it running for indefinite times. (2 Replies)
Learning, stumbling! My progress in shell scripting is slow. Now I have this doubt:
I have the following file (users.txt):
AU0909,on
AU0309,off
AU0209,on
AU0109,off
And this file (userson.txt)
AU0909
AU0209
AU0109
AU0309
I just want to set those users on userson.txt to "off" in... (14 Replies)
I am parsing file for the fields using awk command, first i check 26th field for two characters using substr function if it matches then using for loop on array i search 184th field for 4 chars if it matches then i print the required fields but on execution i get the error, please help...... (5 Replies)
I have written the below PERL script to reprocess messages from a failure queue.
It basically browses all the messages in the failure queue to individual files in a directory and then scans those files to determine the originating queue. The script will then move each message in turn from the... (0 Replies)
Hi,
input:
AAA|1
my script (the function is just an example):
gawk 'BEGIN{FS=OFS="|"}
function repeat(str, n, rep, i){
for(i=1; i<=n; i++)
rep=rep str
return rep
}
{
variable_1=repeat($1,$2)
variable_2=repeat($1,$2+1)
variable_3=repeat($1,$2+3)
... (5 Replies)
Discussion started by: beca123456
5 Replies
LEARN ABOUT MOJAVE
lam
LAM(1) BSD General Commands Manual LAM(1)NAME
lam -- laminate files
SYNOPSIS
lam [-f min.max] [-s sepstring] [-t c] file ...
lam [-p min.max] [-s sepstring] [-t c] file ...
DESCRIPTION
The lam utility copies the named files side by side onto the standard output. The n-th input lines from the input files are considered frag-
ments of the single long n-th output line into which they are assembled. The name `-' means the standard input, and may be repeated.
Normally, each option affects only the file after it. If the option letter is capitalized it affects all subsequent files until it appears
again uncapitalized. The options are described below:
-f min.max
Print line fragments according to the format string min.max, where min is the minimum field width and max the maximum field width.
If min begins with a zero, zeros will be added to make up the field width, and if it begins with a `-', the fragment will be left-
adjusted within the field.
-p min.max
Like -f, but pad this file's field when end-of-file is reached and other files are still active.
-s sepstring
Print sepstring before printing line fragments from the next file. This option may appear after the last file.
-t c The input line terminator is c instead of a newline. The newline normally appended to each output line is omitted.
To print files simultaneously for easy viewing use pr(1).
EXAMPLES
The command
lam file1 file2 file3 file4
joins 4 files together along each line. To merge the lines from four different files use
lam file1 -S "
" file2 file3 file4
Every 2 lines of a file may be joined on one line with
lam - - < file
and a form letter with substitutions keyed by `@' can be done with
lam -t @ letter changes
SEE ALSO join(1), paste(1), pr(1), printf(3)STANDARDS
Some of the functionality of lam is standardized as the paste(1) utility by IEEE Std 1003.2 (``POSIX.2'').
BUGS
The lam utility does not recognize multibyte characters.
BSD August 12, 2004 BSD