Sponsored Content
Full Discussion: PLINK help
Top Forums Shell Programming and Scripting PLINK help Post 302694773 by smitra on Friday 31st of August 2012 11:32:36 AM
Old 08-31-2012
PLINK help

Hi Plink users,
I am very new in GWAS and decided to use PLINK for this. But I am struggling with file formats.
I have one exome data with 200000 SNPs in it. But it is in .txt format. But all the necessary fields are there in different columns.
Can you please suggest me how I can create the plink .bed file?
Is there any direct way to create .bed file from .txt?

I tried to create a .bim and a .fam file following the instruction in PLINK website Binary files (BED/BIM/FAM)
Is there any way to create .bed file from these two (.bim & .fam) files?
Please let em know.
Thanks a lot,
Suparna.
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

How we can use plink?

Hi, How we can use use plink to access unix system using Dos. Could someone send me the commands that can be use in Batch file to call unix system using plink utility. Thanks in advance (0 Replies)
Discussion started by: shekhar_ssm
0 Replies

2. Shell Programming and Scripting

plink and shell script

This is my shell script... test.sh DIRECTORY=/XYZ/PQR if ; then echo "In test.." else echo "lno.." fi when i run this script through a putty its output is: ./test.sh: line 2: [: too many arguments lno.. But when i run the same script using plink its running fine and its... (5 Replies)
Discussion started by: praveen.1
5 Replies

3. Shell Programming and Scripting

Error with Plink

Hello. I have a TCL script that logs in to a server using SSH. As SSH isn't available in windows,I used Plink to do the job.The script works fine on my PC and 2 of my friend's PC. However, on one PC, I get the following error message: "'D:\scripts\plink.exe' is not a Win32 Console... (1 Reply)
Discussion started by: plasmalightwave
1 Replies

4. Shell Programming and Scripting

Putty / Plink help

Im trying C:\Program Files\PUTTY\plink.exe mysite.net -l username -pw mypassword -m restart.sh But the login / password are never sent. If I remove the -m restart.sh it will login I need the command inside restart.sh issued after the login password is completed. THanks (6 Replies)
Discussion started by: Greystone
6 Replies

5. AIX

plink shutdown

Hi, I'm testing out this plink script - which will be executed to shutdown multiple LPARs. This consists from: plink -i /path/ssh/cert/ root@host shutdown -F plink -i /path/ssh/cert/ root@host2 shutdown -F The commands gets executed, however it stops on one host, and does not move... (6 Replies)
Discussion started by: ollie01
6 Replies

6. Shell Programming and Scripting

plink truncating commands

I'm using plink.exe on WinXP to run some commands on Z/OS BASH. My commands are interspersed with echo commands so that I can parse the output and work out what is where. The first hundred or so commands run fine, but then one of them gets truncated. For example: Input: echo :end_logdetail:... (6 Replies)
Discussion started by: PhilHibbs
6 Replies

7. Shell Programming and Scripting

Need help on Plink

Hi All, Iam a newbie to the plink and need your assistance. I have referred some posts but it doesn't helps me much. I have two steps to do. 1. I have a config file which has a list of servers,username and password. 2. I have a shell script in windows which accepts arguments and need to... (0 Replies)
Discussion started by: cskumar
0 Replies

8. Shell Programming and Scripting

Using plink with sudo access

I have similar issue as mentioned in 167174-how-run-script-using-batch-file.html It works good, but the control is not coming back to source i tried adding exit to remote script. Thanks, Suresh (0 Replies)
Discussion started by: snsuresh
0 Replies

9. Windows & DOS: Issues & Discussions

Plink wait problem

Hi, I have run into a problem to which i can't seem to find any solution, posting here is my last resort. Problem: I am using plink to access my router and run a few configuration commands. When in enter configurations mode, instead of sending next command plink keeps on waiting for manual... (7 Replies)
Discussion started by: zaainabbas
7 Replies

10. Windows & DOS: Issues & Discussions

Plink is not working

Hi, I am executing below command from Windows run and it is not working "C:\Program Files (x86)\PuTTY\pageant.exe" "D:\abc_key.ppk" -c "C:\Program Files (x86)\PuTTY\plink.exe" -ssh 172.19.11.134 sh ~/touchfile.sh I have created a .ppk file in the directory specified The plink window... (2 Replies)
Discussion started by: NP1
2 Replies
fam(1M) 																   fam(1M)

NAME
fam - file alteration monitor SYNOPSIS
/usr/etc/fam [ -f | -v | -d ] [ -l | -t NFS_polling_interval ] [ -T idle_timeout ] [ -p program.version ] [ -L ] [ -C ] [ -c config_file ] DESCRIPTION
fam is a server that tracks changes to the filesystem and relays these changes to interested applications. Applications such as fm(1G) and mailbox(1) present an up-to-date view of the filesystem. In the absence of fam, these applications and others like them are forced to poll the filesystem to detect changes. fam is more efficient. Applications can request fam to monitor any files or directories in any filesystem. When fam detects changes to monitored files, it noti- fies the appropriate application. The FAM API provides a programmatic interface to fam; see fam(3X). fam is informed of filesystem changes as they happen by the kernel through the imon(7M) pseudo device driver. If asked to monitor files on an NFS mounted filesystem, fam tries to use fam on the NFS server to monitor files. If fam cannot contact a remote fam, it polls the files instead. fam also polls special files. Normally, fam is started by inetd(1M). It is registered with portmap(1M) as performing the sgi_fam service. OPTIONS
-l Disable polling of NFS files. It does not disable use of remote fam on NFS servers, nor does it disable polling of local files. -t NFS_polling_interval Set the interval for polling files to NFS_polling_interval seconds. The default is six seconds. -T idle_timeout Set the idle timeout interval to idle_timeout. fam exits idle_timeout seconds after its last client disconnects. A value of 0 causes fam to wait indefinitely for new connections. The default is five seconds. -f Remain in the foreground instead of spawning a child and exiting. This option is ignored if fam is started by inetd. -v Turn on verbose messages. -d Enable verbose messages and debug messages. -p program.version Use the specified RPC program and version numbers. -L Local-only mode. fam will only accept requests from clients running on the local machine. This overrides the local_only flag in the configuration file. This option is ignored if fam is started by inetd. -C Compatibility mode. This disables authentication and reduces access security as described under SECURITY below. This overrides the insecure_compatibility flag in the configuration file. -c config_file Read configuration information from the given file rather than the default, which is /etc/fam.conf. CONFIGURATION FILE
In addition to its command-line options, fam's behavior can also be controlled through its configuration file. By default, this is /etc/fam.conf; the -c command-line option can be used to specify an alternate file. Configuration lines are in the format option=value. Lines beginning with # or ! are ignored. fam recognizes the following options: insecure_compatibility If set to true, this disables authentication and reduces access security as described under SECURITY below. This is false by default. Setting this option to true is the same as using the -C command-line option. untrusted_user This is the user name or UID of the user account which fam will use for unauthenticated clients. If a file can't be stat'ed by this user, fam will not tell unauthenticated clients about the file's existence. If an untrusted user is not given in the configuration file, fam will write an error message to the system log and terminate. local_only If set to true, fam will ignore requests from remote fams. This is false by default. Setting this option to true is the same as using the -L command-line option. This option is ignored if fam is started by inetd. xtab_verification If set to true, fam will check the list of exported filesystems when remote requests are received to verify that the requests fall on filesystems which are exported to the requesting hosts. This is true by default. If this option is set to false, fam will service remote requests without attempting to perform the verification. If the local_only configuration option or -L command-line option is used, xtab_verification has no effect. SECURITY
For backward compatibility, the -C command-line option and insecure_compatibility configuration option can be used to disable authentica- tion. Configuring fam this way opens a publically known security weakness whereby a "rogue client" can obtain the names of all the files and directories on the system. Note that fam never opens the files it's monitoring, and cannot be used by a rogue client to read the contents of any file on the system. fam only gives out the names of monitored files, and only monitors files which the client can stat(1M). Users can stat a file without hav- ing read permission on it as long as they have search permission on the directory containing it. FILES
/etc/fam.conf SEE ALSO
inetd(1M), portmap(1M), fam(3X), imon(7M), stat(1M). Silicon Graphics 0a
All times are GMT -4. The time now is 11:58 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy