Hello,
I am trying to create a matrix of 0's and 1's depending on whether a gene and sample name are found in the same line in a file called results.txt. An example of the results.txt file is (tab-delimited):
The matrix should look like this:
where 1 = 'match found for both gene and sample' and 0 for 'no match'.
My code reads in three files: GenesList.txt (gene names), SampleList.txt (Sample names), and the results.txt file. The output matrix should be Matrix.out.
The multiple grep condition on a single line does not seem to be working properly for me, or maybe I have a problem with my If statement??
For the resultant matrix I expect for any row to have both 0's and 1's, but I end up with an entire matrix of only 1's or only 0's. What am I missing from this bash script?
I'm just trying to make a script that runs in command line to echo each line in a text file. Everything i found on google is telling me to do it like this but when I run it it just echos removethese.txt and thats it. Anyone know what im doing wrong?
for i in removethese.txt; do echo $i; done
... (4 Replies)
Hi,
I'm having a problem with the while loop in bash. I try the following script:
#!/bin/bash
while true
do
echo "test"
done
When I try this, it gives me this error:
while: Too few arguments.
What am I doing wrong?
Thanks (5 Replies)
I have file named script1 as follows:
#!/bin/bash
count="0"
echo "hello"
echo "$count"
while
do
echo "$count"
count=`expr $count + 1`
done
-----------
when I run it, I get
./script1: line 9: syntax error near unexpected token `done'
./script1: line 9: `done'
I... (6 Replies)
Hello,
I've got next problem:
I want to examine at the beginning of a script in an if loop that:
1. Is there 4 parameters given
2. If first state is true then: is there switches -e and -d?
3. At the end, how can i indentify them as variebles regardlees to its order.
I was thinking like... (2 Replies)
I'm trying to do a script where I want to see if all users home directories are only writable by owner. However, in my script I do not know how to implement the for loop so that all directories are checked. In mine, I am only checking the permissions for the first directory found. I do know that a... (3 Replies)
Hi,
I have a loop running until a variable L that is read previously in the full script. I'd like to grep some information in an input file at a line that contains the value of the loop parameter $i.
I've tried to use grep, but the problem is nothing is written in the FILE files. It seems grep... (5 Replies)
Dear mentors, I just need little explanation regarding for loop to give input to awk script
for file in `ls *.txt |sort -t"_" -k2n,2`; do
awk script $file
done
which sorts file in order, and will input one after another file in order to awk script
suppose if I have to input 2 or... (4 Replies)
Dear All,
I have problem with generalizing my code and I can't see where the problem is.
I have a main.txt file that has all the information and then I have 4 folders (headoffice, branch, management, office) that each have a 2 of files keep.txt and throw.txt and each of them have few lines... (3 Replies)
Hi Everybody,
I'm a newbie to shell scripting, and I'd appreciate some help. I have a bunch of .txt files that have some unwanted content. I want to remove lines 1-3 and 1028-1098.
#!/bin/bash
for '*.txt' in <path to folder>
do
sed '1,3 d' "$f";
sed '1028,1098 d' "$f";
done
I... (2 Replies)
Dear all,
Please help with the following.
I have a file, let's call it data.txt, that has 3 columns and approx 700,000 lines, and looks like this:
rs1234 A C
rs1236 T G
rs2345 G T
Please use code tags as required by forum rules!
I have a second file, called reference.txt,... (1 Reply)
Discussion started by: aberg
1 Replies
LEARN ABOUT LINUX
zegrep
ZGREP(1) General Commands Manual ZGREP(1)NAME
zgrep - search possibly compressed files for a regular expression
SYNOPSIS
zgrep [ grep_options ] [ -e ] pattern filename...
DESCRIPTION
Zgrep invokes grep on compressed or gzipped files. These grep options will cause zgrep to terminate with an error code:
(-[drRzZ]|--di*|--exc*|--inc*|--rec*|--nu*). All other options specified are passed directly to grep. If no file is specified, then the
standard input is decompressed if necessary and fed to grep. Otherwise the given files are uncompressed if necessary and fed to grep.
If the GREP environment variable is set, zgrep uses it as the grep program to be invoked.
EXIT CODE
2 - An option that is not supported was specified.
AUTHOR
Charles Levert (charles@comm.polymtl.ca)
SEE ALSO grep(1), gzexe(1), gzip(1), zdiff(1), zforce(1), zmore(1), znew(1)ZGREP(1)