10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
In the bash menu below if the variant that is inputted is in the format NM_004004.3:c.274G>T the below works perfectly. My question is if the variant inputted isNM_004004.3:-c.274G>T or NM_004004.3:+c.274G>T then the code as is will throw an error due to a biological issue. Is it possible to to... (1 Reply)
Discussion started by: cmccabe
1 Replies
2. Shell Programming and Scripting
I have a special case that awk could be used but I do not have the skill. Trying to create a final output file (indel_parse.txt) that is created from using some information from each of the two files (attached).
parse rules:
The header is skipped FNR>1
1. 4 zeros after the NC_ (not... (2 Replies)
Discussion started by: cmccabe
2 Replies
3. Shell Programming and Scripting
Hi all,
I have a list which I want to search in another file.
I can do that using
grep -f
but the search is failing due to special characters, how do I solve this?
One row in that list is
amino-acid permease inda1 gb|EDU41782.1| amino-acid permease inda1 Input file to be searched... (2 Replies)
Discussion started by: gina.lizar
2 Replies
4. Shell Programming and Scripting
14`~abc`~9`~11
14`~abc`~9`~10
36`~ee`~7`~9
36`~ee`~8`~9
58`~rtt`~12`~7
70`~gff`~13`~8
86`~tyu`~6`~12
86`~tyu`~6`~13
92`~mjh`~5`~6
28`~jkl`~10`~DNA
32`~mjk`~SNA`~5
82`~jkli`~11`~DNA
------------------------------------
Field Seperator: `~
The concept is to start with SNA in the 3rd... (8 Replies)
Discussion started by: barath
8 Replies
5. Shell Programming and Scripting
complinagetest () #function name
{
if ;then
rm complins.dat
fi
touch complins.dat
i=0
while read line
do
if ; then
va=`grep -w "$line" datalins1.dat | awk BEGIN'{FS="\`~"}{if ( $3=="'$line'" ) {print $4}}'`
i=$(($i+1))
varits=$(echo $va|awk -v varif="$i" '{print... (1 Reply)
Discussion started by: amitpaul01
1 Replies
6. UNIX for Dummies Questions & Answers
In bash shell, how we can avoid the commands getting recorded in history file.
One way i can think of is :
export HISTSIZE=0
Is there any other way to achieve this?
Thanks (1 Reply)
Discussion started by: pandeesh
1 Replies
7. Shell Programming and Scripting
Hi. Let me start saying that i am kinda new to bash, and have few skills in programming. I've been advised to use bash to manipulate large .csv files. I've been able to do some data filtering using fors, grep and tail commands. That was kinda easy seeing examples. But now i need to do some hard... (1 Reply)
Discussion started by: jmarmitt
1 Replies
8. Shell Programming and Scripting
I made menu script for users so they can run other script without going in shell just from menu.
But i must control their input.
These are criteria:
Input must have 4 signs
First two signs are always lower case letters
Input shall not have some special signs just letters and numbers
... (1 Reply)
Discussion started by: waso
1 Replies
9. UNIX for Dummies Questions & Answers
hello all
i have a big problems for me
if i have more files as example
test.ghrt.part01.rar
test.ghrt.part02.rar
test.ghrt.part03.rar
test.ghrt.part04.rar
test.ghrt.part05.rar
test.ghrt.part06.rar
test.ghrt.part07.rar
test.ghrt.part08.rar
test.ghrt.part09.rar
test.ghrt.part10.rar... (13 Replies)
Discussion started by: ateya
13 Replies
10. UNIX for Dummies Questions & Answers
Hello,
Today, as a root user, i want to copy recursively all files and diretories in a source directory to a destination directory using the following command,
cp -r /home/smith/* /home/bob/
However, I carelessly missed the '*' out when I executed the command.
Now, i noticed a... (1 Reply)
Discussion started by: cy163
1 Replies
