I am using the following code to extract sequences that contain dashes
Now, I actually need to do the opposite. I need to print the sequences that do not contain dashes. Moreover, I also would like to exclude the sequences that contain *. So the expected outfile is the following one:
suppose
fileA
kanika123ABC 1222222222222222
raciat5678ty 1221123333331121
jessica78ulllo 2233243223333333
so output shud be print only first 10 characters in series and rest remain same
kanika123A 1222222222222222
raciat5678 1221123333331121
jessica78u ... (1 Reply)
Hi I made a post earlier but now my problem has become a lot more complicated.
So I have a file that looks like this:
Name 1 13 94 1 AGGTT
Name 1 31 44 1 TTCCG
Name 1 13 94 2 AAAAATTTT
Name 1 41 47 2 GGGGGGGGGGG So the file is tab delimited and what I want to do is find... (8 Replies)
Dear friends,
hello to everyone. I am new to this forum.
I have a set of data where I need to find the repitition of series as below
data format:
0001230000456000001230000456
each digit can be separated by any delimeter
I need to find out the starting point (index) of '123' and '456'
I... (2 Replies)
I have two LARGE files of data more than 20,000 line each, file-1 and file-2, and I wish to do the following if possible:
file-1
1 2 5 7 9
2 4 6 3 8 9
4 6 8 9 3 2 1 3
1 2
.
.
.
file-2
1 2 3
2 5 7
5 7 3
7 9 4
. (5 Replies)
sed -e "s// /g" old.txt > new.txt
While I do know some control characters need to be escaped, can normal characters also be escaped and still work the same way? Basically I do not know all control characters that have a special meaning, for example, ?, ., % have a meaning and have to be escaped... (11 Replies)
Hi all.
I have a .txt file that I need to sort it
My file is like:
1- 88 chain0 MASTER (FF-TE) FFFF 1962510 /TCK T FD2TQHVTT1 /jtagc/jtag_instreg/updateinstr_reg_1 dff1 (TI,SO)
2- ... (10 Replies)
I am trying to find a specific set of characters in a long file. I only want to find the characters in column 265 for 4 bytes.
Is there a search for that? I tried cut but couldn't get it to work.
Ex. I want to find '9999' in column 265 for 4 bytes. If it is in there, I want it to print... (12 Replies)
Hi all, I need help.
I have an input text file (input.txt) like this:
21 GTGCAACACCGTCTTGAGAGG 50
21 GACCGAGACAGAATGAAAATC 73
21 CGGGTCTGTAGTAGCAAACGC 108
21 CGAAAAATGAACCCCTTTATC 220
21 CGTGATCCTGTTGAAGGGTCG 259
Now I need to count A/T/G/C numbers at each character location in column... (2 Replies)
Hi All,
Assuming i have got a file test.dat which has contains as follows:
Unix = abc def fgt jug
111 2222 3333
Linux = gggg pppp qqq
C# = ccc ffff llll
I would like to traverse through the file, get the 1st occurance of "=" and then need to get the sting... (22 Replies)
Hi
I have a file which is tab-delimited. Now, I'd like to print the lines which have "chr6" string in both first and second columns. Could anybody help? (3 Replies)
Discussion started by: a_bahreini
3 Replies
LEARN ABOUT CENTOS
shell-quote
SHELL-QUOTE(1) User Contributed Perl Documentation SHELL-QUOTE(1)NAME
shell-quote - quote arguments for safe use, unmodified in a shell command
SYNOPSIS
shell-quote [switch]... arg...
DESCRIPTION
shell-quote lets you pass arbitrary strings through the shell so that they won't be changed by the shell. This lets you process commands
or files with embedded white space or shell globbing characters safely. Here are a few examples.
EXAMPLES
ssh preserving args
When running a remote command with ssh, ssh doesn't preserve the separate arguments it receives. It just joins them with spaces and
passes them to "$SHELL -c". This doesn't work as intended:
ssh host touch 'hi there' # fails
It creates 2 files, hi and there. Instead, do this:
cmd=`shell-quote touch 'hi there'`
ssh host "$cmd"
This gives you just 1 file, hi there.
process find output
It's not ordinarily possible to process an arbitrary list of files output by find with a shell script. Anything you put in $IFS to
split up the output could legitimately be in a file's name. Here's how you can do it using shell-quote:
eval set -- `find -type f -print0 | xargs -0 shell-quote --`
debug shell scripts
shell-quote is better than echo for debugging shell scripts.
debug() {
[ -z "$debug" ] || shell-quote "debug:" "$@"
}
With echo you can't tell the difference between "debug 'foo bar'" and "debug foo bar", but with shell-quote you can.
save a command for later
shell-quote can be used to build up a shell command to run later. Say you want the user to be able to give you switches for a command
you're going to run. If you don't want the switches to be re-evaluated by the shell (which is usually a good idea, else there are
things the user can't pass through), you can do something like this:
user_switches=
while [ $# != 0 ]
do
case x$1 in
x--pass-through)
[ $# -gt 1 ] || die "need an argument for $1"
user_switches="$user_switches "`shell-quote -- "$2"`
shift;;
# process other switches
esac
shift
done
# later
eval "shell-quote some-command $user_switches my args"
OPTIONS --debug
Turn debugging on.
--help
Show the usage message and die.
--version
Show the version number and exit.
AVAILABILITY
The code is licensed under the GNU GPL. Check http://www.argon.org/~roderick/ or CPAN for updated versions.
AUTHOR
Roderick Schertler <roderick@argon.org>
perl v5.16.3 2010-06-11 SHELL-QUOTE(1)