Hi all,
I have difficulty to solve the followign problem.
mydata:
StartPoint EndPoint
22 55
2222 2230
33 66
44 58
222 240
11 25
22 60
33 45
The union of above... (2 Replies)
Dear Gurus,
I have 57 tab-delimited different text files, each one containing entries in 3 columns. The first column in each file contains names of objects. Some names are present in more than one file. I would like to find those names and store them in a separate text file, preferably with a... (6 Replies)
Hi, I have a file1 of many long sequences, each preceded by a unique header line. file2 is 3-columns list: headers name, start position, end position. I'd like to extract the sequence region of file1 specified in file2.
Based on a post elsewhere, I found the code:
awk... (2 Replies)
Discussion started by: pathunkathunk
2 Replies
4. Forum Support Area for Unregistered Users & Account Problems
The forums have been seeing a sharp increase in spam bots, forum robots, and malicious registrations from certain countries. If you have been directed to this thread due to a "No Permission Error" when trying to register please post in this thread and request permission to register, including... (1 Reply)
Hi I have 2 files; usually the end position in the file1 is the start position in the file2 and the end position in file2 will be the start position in file1 (flanks)
file1
Id start end
aaa1 0 3000070
aaa1 3095270 3095341
aaa1 3100822 3100894
aaa1 ... (1 Reply)
Hello, here I am posting my query again with modified data input files.
see my query is :
i have two input files file1 and file2.
file1 is smalldata.fasta
>gi|546671471|gb|AWWX01449637.1| Bubalus bubalis breed Mediterranean WGS:AWWX01:contig449636, whole genome shotgun sequence... (20 Replies)
Hi,
I have been trying to retrieve the names of files present in a directory one by one but the names of files are getting overlapped on one another.
I tried the below command.
ls -1 > filename
please help me in getting the file names line by line without overlapping. I am using korn... (6 Replies)
Hi all,
I have a file like this I want to extract only those regions which are big and continous
chr1 3280000 3440000
chr1 3440000 3920000
chr1 3600000 3920000 # region coming within the 3440000 3920000. so i don't want it to be printed in output
chr1 3920000 4800000
chr1 ... (2 Replies)
Discussion started by: amrutha_sastry
2 Replies
LEARN ABOUT DEBIAN
shell-quote
SHELL-QUOTE(1p) User Contributed Perl Documentation SHELL-QUOTE(1p)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 v5.8.4 2005-05-03 SHELL-QUOTE(1p)