Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: awk to update unknown value in file using range of another
Top Forums Shell Programming and Scripting awk to update unknown value in file using range of another Post 302986041 by Don Cragun on Saturday 19th of November 2016 01:02:29 AM
Old 11-19-2016
Yes, clearly you need to use the split() call to define the array a[] that you are using, but (as you noted) you can't use the elements of that array as subscripts in another array because the values are not unique. Instead of you an array of minimum values and an array of maximum values indexed by the line number in your first file.

But, I don't understand the output that you say should be produced. Why do you want the output to be (with all occurrences of four spaces in your output replaced by <tab> characters):
Code:
chr1	3649533	3649653	chr1:3649533-3649653	.	TP73
chr1	4736396	4736516	chr1:4736396-4736516	.	AJAP1
chr1	5923314	5923434	chr1:5923314-5923434	.	NPHP4
chr1	9161991	9162111	chr1:9161991-9162111	.	unknown
chr1	9162050	9162051	chr1:9162050-9162051	.	rs6697376

instead of:
Code:
chr1	3649533	3649653	chr1:3649533-3649653	.	TP73
chr1	4736396	4736516	chr1:4736396-4736516	.	AJAP1
chr1	5923314	5923434	chr1:5923314-5923434	.	NPHP4
chr1	9161991	9162111	chr1:9161991-9162111	.	GPR157
chr1	9162050	9162051	chr1:9162050-9162051	.	rs6697376

?
This User Gave Thanks to Don Cragun For This Post:
cmccabe
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk to update file if value within range

I have a file (sorted_unknown) with ~1400 $5 values before the - that are "unknown". What I am trying to do is use the text in $2 of (sort_targets) to update those "unknown" values in the (sorted_unknown). In $1 of (sort_targets) there are a set of numbers that can be used to update the "unknown"... (8 Replies)
Discussion started by: cmccabe
8 Replies

2. Shell Programming and Scripting

awk match to update contents of file

I am trying to match $1 in file1 with $2 in file2. If a match is found then $3 and $4 of file2 are copied to file1. Both files are tab-delimeted and I am getting a syntax error and would also like to update file1 in-place without creating a new file, but am not sure how. Thank you :). file1 ... (19 Replies)
Discussion started by: cmccabe
19 Replies

3. Shell Programming and Scripting

awk to lookup section of file in a range of another file

In the below, I am trying to lookup $1 and $2 from file1, in a range search using $1 $2 $3 of file2. If the search key from file1 is found in file2, then the word low is printed in the last field of that line in the updated file1. Only the last section of file1 needs to be searched, but I am not... (6 Replies)
Discussion started by: cmccabe
6 Replies

4. Shell Programming and Scripting

awk to lookup value in one file in another range

I am trying to update the below awk, kindly provided by @RavinderSingh13, to update each line of file1 with either Low or No Low based on matching $2 of file1 to a range in $2 and $3 of file2. If the $2 value in file1 matches the range in file2 then that line is Low, otherwise it is No Low in the... (3 Replies)
Discussion started by: cmccabe
3 Replies

5. Shell Programming and Scripting

awk to filter file using range in another file

I have a very large tab-delimited, ~2GB file2 that I am trying to filter using $2 of file1. If $2 of file1 is in the range of $2 and $3 in file1 then the entire line of file2 is outputed. If the range match is not found then that line is skipped. The awk below does run but no output results. ... (3 Replies)
Discussion started by: cmccabe
3 Replies

6. Shell Programming and Scripting

awk to update file based on 5 conditions

I am trying to use awk to update the below tab-delimited file based on 5 different rules/conditions. The final output is also tab-delimited and each line in the file will meet one of the conditions. My attemp is below as well though I am not very confident in it. Thank you :). Condition 1: The... (10 Replies)
Discussion started by: cmccabe
10 Replies

7. Shell Programming and Scripting

awk to print out lines that do not fall between range in file

In the awk below I am trying to print out those lines in file2 that are no between $2 and $3 in file1. Both files are tab-delimeted and I think it's close but currently it is printeing out the matches. The --- are not part of the files they are just to show what lines match or fall into the range... (6 Replies)
Discussion started by: cmccabe
6 Replies

8. Shell Programming and Scripting

awk to update file with sum of matching fields in another file

In the awk below I am trying to add a penalty to a score to each matching $1 in file2 based on the sum of $3+$4 (variable TL) from file1. Then the $4 value in file1 is divided by TL and multiplied by 100 (this valvue is variable S). Finally, $2 in file2 - S gives the updated $2 result in file2.... (2 Replies)
Discussion started by: cmccabe
2 Replies

9. UNIX for Beginners Questions & Answers

How to sum value of a column by range defined in another file awk?

I have two files, file1.table is the count table, and the other is the range condition file2.range. file1.table chr start end count N1 0 48 1 N1 48 181 2 N1 181 193 0 N1 193 326 2 N1 326 457 0 N1 457 471 1 N1 471 590 2 N1 590 604 1 N1 604 752 1 N1 752 875 1 file2.range... (12 Replies)
Discussion started by: yifangt
12 Replies

10. UNIX for Beginners Questions & Answers

awk to update file with partial matching line in another file and append text

In the awk below I am trying to cp and paste each matching line in f2 to $3 in f1 if $2 of f1 is in the line in f2 somewhere. There will always be a match (usually more then 1) and my actual data is much larger (several hundreds of lines) in both f1 and f2. When the line in f2 is pasted to $3 in... (4 Replies)
Discussion started by: cmccabe
4 Replies

LEARN ABOUT DEBIAN

colorgccrc

COLORGCCRC(5)							File Formats Manual						     COLORGCCRC(5)

NAME

       colorgccrc - configuration file for colorgcc

DESCRIPTION

       A colorgccrc configuration file is used to configure the highlighting of the compiler output from colorgcc.

SYNTAX

       Each  line  consists  of  a  keyword  designating  a configuration variable.  The keyword is followed by `:' and then one or several values
       (depending on the keyword).  Lines beginning with a hash mark `#' are comments.

CONFIGURATION VARIABLES

       g++ | gcc | c++ | cc | g77 | gcj | gnat | gpc
	      Specifies the paths to the compilers.  Takes one value; a path to the compiler.

       nocolor
	      Specifies what terminal types colorization should be disabled on.  Takes one or several values, separated by whitespace.

       srcColor
	      Specifies the highlighting attributes source-code should be given.  Takes one or several color attributes.  See  the  section  COLOR
	      ATTRIBUTES for more information.

       introColor
	      Specifies  the  highlighting  attributes	for normal compiler output.  Takes one or several color attributes.  See the section COLOR
	      ATTRIBUTES for more information.

       warningFileNameColor | errorFileNameColor
	      Specifies the highlighting attributes for the filename in a  warning  or	an  error,  respectively.   Takes  one	or  several  color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

       warningNumberColor | errorNumberColor
	      Specifies  the  highlighting  attributes	for  the  line-number  in a warning or an error, respectively.	Takes one or several color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

       warningMessageColor | errorMessageColor
	      Specifies the highlighting attributes for the message-text in a warning or an error,  respectively.   Takes  one	or  several  color
	      attributes.  See the section COLOR ATTRIBUTES for more information.

COLOR ATTRIBUTES

       The following attributes are valid for highlighting.

       clear, reset

       bold, underline, underscore, blink, reverse, concealed

       black, red, green, yellow, blue, magenta, cyan, white

       on_black, on_red, on_green, on_yellow, on_blue, on_magenta, on_cyan, on_white

SEE ALSO

       gcc(1), colorgcc(1)

HISTORY

       Jan 15 2003: Initial version of this manual-page.

REPORTING BUGS

       Report bugs to <jmoyers@geeks.com>

AUTHORS

       Jamie Moyers <jmoyers@geeks.com> is the author of colorgcc.

       This  manual  page  was	written  by Joe Wreschnig <piman@sacredchao.net>, and modified by David Weinehall <tao@debian.org>, for the Debian
       GNU/Linux system (but may be used by others).

COPYRIGHT

       Copyright (C) 2003 Jamie Moyers
       This is free software; see the source for copying conditions.  There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU-
       LAR PURPOSE.

								   Jan 15, 2003 						     COLORGCCRC(5)
All times are GMT -4. The time now is 07:25 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy