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Full Discussion: Matrix parsing help !
Top Forums Programming Matrix parsing help ! Post 302586839 by mchimich on Tuesday 3rd of January 2012 12:08:41 PM
Old 01-03-2012
OK sir ctsgnb ! The input is (just the beginning because the original file contain more than 100,000 lines ! ):
Code:
chromosome07_194379   chromosome01_168057       0.975
chromosome01_100293   chromosome01_168057       0.969
chromosome01_100293   chromosome07_194379       0.969
chromosome01_29385    chromosome01_168057       0.856
chromosome01_29385    chromosome07_194379       0.856
chromosome01_29385    chromosome01_100293       0.861
chromosome08_116839   chromosome01_168057       0.78
chromosome08_116839   chromosome01_100293       0.786
chromosome08_116839   chromosome01_293853       0.946

and the output file must be like that :

Code:
chromosome07_194379 chromosome01_168057 chromosome01_100293 chromosome01_29385 chromosome08_116839 chromosome01_293853

This is one group even if the IDs in bold charachter don't share more than 80% of identity
a very simple case is when you have A--B--C association but the A and C don't share enough identity to be considered together but is one continue group . I don't now if i'm clear ctsgnb
Thanks again for your help

Last edited by vgersh99; 01-03-2012 at 01:41 PM.. Reason: fixed code tags
 

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SETGID(2)						     Linux Programmer's Manual							 SETGID(2)

NAME
setgid - set group identity SYNOPSIS
#include <sys/types.h> #include <unistd.h> int setgid(gid_t gid); DESCRIPTION
setgid() sets the effective group ID of the calling process. If the calling process is privileged (has the CAP_SETGID capability in its user namespace), the real GID and saved set-group-ID are also set. Under Linux, setgid() is implemented like the POSIX version with the _POSIX_SAVED_IDS feature. This allows a set-group-ID program that is not set-user-ID-root to drop all of its group privileges, do some un-privileged work, and then reengage the original effective group ID in a secure manner. RETURN VALUE
On success, zero is returned. On error, -1 is returned, and errno is set appropriately. ERRORS
EINVAL The group ID specified in gid is not valid in this user namespace. EPERM The calling process is not privileged (does not have the CAP_SETGID capability), and gid does not match the real group ID or saved set-group-ID of the calling process. CONFORMING TO
POSIX.1-2001, POSIX.1-2008, SVr4. NOTES
The original Linux setgid() system call supported only 16-bit group IDs. Subsequently, Linux 2.4 added setgid32() supporting 32-bit IDs. The glibc setgid() wrapper function transparently deals with the variation across kernel versions. C library/kernel differences At the kernel level, user IDs and group IDs are a per-thread attribute. However, POSIX requires that all threads in a process share the same credentials. The NPTL threading implementation handles the POSIX requirements by providing wrapper functions for the various system calls that change process UIDs and GIDs. These wrapper functions (including the one for setgid()) employ a signal-based technique to ensure that when one thread changes credentials, all of the other threads in the process also change their credentials. For details, see nptl(7). SEE ALSO
getgid(2), setegid(2), setregid(2), capabilities(7), credentials(7), user_namespaces(7) COLOPHON
This page is part of release 4.15 of the Linux man-pages project. A description of the project, information about reporting bugs, and the latest version of this page, can be found at https://www.kernel.org/doc/man-pages/. Linux 2017-09-15 SETGID(2)
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