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Top Forums UNIX for Advanced & Expert Users Map snps into a ref gene file Post 302989932 by Don Cragun on Thursday 19th of January 2017 10:24:56 PM
Old 01-19-2017
No you have not. None of the data shown in the columns of the output you said you wanted in post #5 and in post #7 (even if the asterisks are removed) in this thread:
Code:
genename   SNPID   chrom   position   txstart   txend

show up anywhere in either of the sample input files shown in post #1 except for the chrom field.

This thread is closed!

Please consider opening a new thread where you show us two small sample input files and show us the exact output that you want your script to produce from those sample input files. Make sure that the data given in those files includes data that tests all of your corner cases and be sure that your description clearly specifies what should happen if multiple values match, what should happen if no values match, what should happen if one value matches, and any special cases that haven't been identified so far by this list.
This User Gave Thanks to Don Cragun For This Post:
 

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setfiles(8)															       setfiles(8)

NAME
setfiles - set file SELinux security contexts. SYNOPSIS
setfiles [-c policy ] [-d] [-l] [-n] [-e directory ] [-o filename ] [-q] [-s] [-v] [-vv|-p] [-W] [-F] spec_file pathname... DESCRIPTION
This manual page describes the setfiles program. This program is primarily used to initialize the security context database (extended attributes) on one or more filesystems. This program is initially run as part of the SE Linux installation process. It can also be run at any time to correct errors, to add support for new policy, or with the -n option it can just check whether the file contexts are all as you expect. It is the same executable as setfiles but operates in a slightly different manner depending on it's argv[0]. OPTIONS
-c check the validity of the contexts against the specified binary policy. -d show what specification matched each file. -l log changes in file labels to syslog. -n don't change any file labels. -p show progress by printing * every 1000 files. -q suppress non-error output. -r rootpath use an alternate root path -e directory directory to exclude (repeat option for more than one directory.) -F Force reset of context to match file_context for customizable files -o filename save list of files with incorrect context in filename. -s take a list of files from standard input instead of using a pathname on the command line. -v show changes in file labels, if type or role are changing. -vv show changes in file labels, if type, role, or user are changing. -p show a progress indication in the form of one dot per 1000 files. -W display warnings about entries that had no matching files. -0 Input items are terminated by a null character instead of by whitespace, and the quotes and backslash are not special (every char- acter is taken literally). Disables the end of file string, which is treated like any other argument. Useful when input items might contain white space, quote marks, or backslashes.The GNU find -print0 option produces input suitable for this mode. ARGUMENTS
spec_file The specification file which contains lines of the following form regexp [ -type ] ( context | <<none>> ) The regular expression is anchored at both ends. The optional type field specifies the file type as shown in the mode field by the ls(1) program, e.g. -- to match only regular files or -d to match only directories. The context can be an ordinary security context or the string <<none>> to specify that the file is not to have its context changed. The last matching specification is used. If there are multiple hard links to a file that match different specifications and those specifi- cations indicate different security contexts, then a warning is displayed but the file is still labeled based on the last matching specifi- cation other than <<none>>. pathname... The pathname for the root directory of each file system to be relabeled. Not used if the -s option is used. AUTHOR
This man page was written by Russell Coker <russell@coker.com.au>. The program was written by Stephen Smalley <sds@epoch.ncsc.mil> SEE ALSO
load_policy(8), checkpolicy(8) 2002031409 setfiles(8)
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