10-10-2009
Hello again,
Again, I apologize for the confsion. I made a mistake in the first post, the letters should be recoded to -1, 0, 1. This is the tricky part. I need to recode the letters on a per column, alphabetical order basis. There are several different combinations that can occur within a column:
AA, AC, CC = -1, 0, 1
AA, AG, GG = -1, 0, 1
AA, AT, TT = -1, 0, 1
CC, CG, GG = -1, 0, 1
CC, CT, TT = -1, 0, 1
GG, GT, TT = -1, 0, 1
Therefore anything with a mixed data point (AC, AG, AT, CG, CT, GT) will ALWAYS = 0, AA will ALWAYS = -1, and TT will ALWAYS = 1. The problem come when recoding CC and GG. As you can see, in some rows CC will come first in the alphabet and will be recoded as -1 (When the combo is CC, CG, GG) . However, in some columns CC does not come first in the alphabet and will be coded as 1 (when the combo is AA, AC, CC). The same problem occurs with GG. IS there any solution to this issue? I hope I explained it better this time!!
Thank you so much for your patience!!
10 More Discussions You Might Find Interesting
1. Shell Programming and Scripting
suppose u have a file which consist of many data points separated by asterisk
Question is to extract third part in each line .
0.0002*0.003*-0.93939*0.0202*0.322*0.3332*0.2222*0.22020
0.003*0.3333*0.33322*-0.2220*0.3030*0.2222*0.3331*-0.3030
0.0393*0.3039*-0.03038*0.033*0.4033*0.30384*0.4048... (5 Replies)
Discussion started by: cdfd123
5 Replies
2. Shell Programming and Scripting
I have a file that has been partially recoded so that data points that were formerly letter combinations are now -1, 0, or 1. I need to finish recoding the GG and CC data points. The file looks like this:
ID 1 2 3 4 5 6 7 8
83845676 0 0 0 0 CC -1 CC CC
838469. -1 -1 1 GG CC 0 CC 1
83847041... (10 Replies)
Discussion started by: doobedoo
10 Replies
3. Shell Programming and Scripting
Hi All I have a data set like this tab delimited:
weft fgr-1 345 -1 fgrythdgd
weft fgr-3 456 -2 ghjdklflllff
weft fgr-11 456 -3 ghtjuffl
weft fgr-1 213 -2 ghtyjdkl
weft fgr-34 567 -5 fghytkflf
frgt fgr-36 567 -1 ghrjufjf
frgt fgr-45 678 -2 ghjruir
frgt fgr-34 546 -5 gjjjgkldlld
frgt... (4 Replies)
Discussion started by: Lucky Ali
4 Replies
4. UNIX for Dummies Questions & Answers
hiii, Help me out..i have a huge set of data stored in a file.This file has has 2 columns which is latitude & longitude of a region. Now i have a program which asks for the number of points & based on this number it asks the user to enter that latitude & longitude values which are in the same... (7 Replies)
Discussion started by: reva
7 Replies
5. Programming
Hi,
I am trying to arrange my graphs with GNUPLOT. Although it looked like simple at the beginning, I could not figure out an answer for the following: I want to change the style of my data points (not the line, just exact data points) The terminal assigns first + and then x to them but what I... (0 Replies)
Discussion started by: natasha
0 Replies
6. Shell Programming and Scripting
Hi,
I have a file with one column data (sample below) and I am trying to write a shell script to calculate the difference between consecutive data valuse i.e
Var = Ni -N(i-1)
0.3141
-3.6595
0.9171
5.2001
3.5331
3.7022
-6.1087
-5.1039
-9.8144
1.6516
-2.725
3.982
7.769
8.88 (5 Replies)
Discussion started by: malandisa
5 Replies
7. UNIX for Dummies Questions & Answers
Hi, I need help on finding the value of my data that encompasses certain percentage of my total data points (n). Attached is an example of my data, n=30. What I want to do is for instance is find the minimum threshold that still encompasses 60% (n=18), 70% (n=21) and 80% (n=24).
manually to... (4 Replies)
Discussion started by: ida1215
4 Replies
8. Shell Programming and Scripting
I have a text file that shows the output of my solar inverters. I want to separate this into sections. overview , device 1 , device 2 , device 3. Each device has different number of lines. but they all have unique starting points. Overview starts with 6 #'s, Devices have 4#'s and their data starts... (6 Replies)
Discussion started by: Mikey
6 Replies
9. Shell Programming and Scripting
Hi, I was wondering if someone would be able to help with extrapolating information from a file and filling an existing matrix with that information.
I have made a matrix like this (file 1):
A B C D
1
2
3
4
I have another file with data like this (file 2):
1 A
1 C
3 C
4 B... (1 Reply)
Discussion started by: hubleo
1 Replies
10. Shell Programming and Scripting
I need to rank a large number of data points that exist in multiple files. My data points (Column 3) are based on unique values in columns 1 and 2. I need to rank the values that are in File 1, Column 3.
For instance:
Input File 1
AAA BBB 10
CCC DDD 16
EEE FFF 20
Input File 2
... (47 Replies)
Discussion started by: ncwxpanther
47 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)