Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: awk to combine matches and use a field to adjust coordinates in other fields
Top Forums Shell Programming and Scripting awk to combine matches and use a field to adjust coordinates in other fields Post 302977606 by RavinderSingh13 on Wednesday 20th of July 2016 11:47:52 AM
Old 07-20-2016
Hello cmccabe,

Could you please try following and let me know if this helps you.
Code:
awk 'FNR==NR{S[$4]++;next} ($4 in S){if(S[$4]>1){print $1 OFS $2 OFS $2+S[$4] OFS $5;} else {if($6==1){print $1 OFS $2 OFS $2 OFS $5} else {print $1 OFS $2+$6 OFS $2+$6 OFS $5}};delete S[$4]}'   Input_file  Input_file

Output will be as follows.
Code:
chrX 110961329 110961334 ALG13
chr2 50573818 50573822 NRXN1
chrX 135080256 135080256 SLC9A6
chr18 53298529 53298529 TCF4

Thanks,
R. Singh
This User Gave Thanks to RavinderSingh13 For This Post:
cmccabe
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk to sum specific field when pattern matches

Trying to sum field #6 when field #2 matches string as follows: Input data: 2010-09-18-20.24.44.206117 UOWEXEC db2bp DB2XYZ hostname 1 2010-09-18-20.24.44.206117 UOWWAIT db2bp DB2XYZ hostname ... (3 Replies)
Discussion started by: ux4me
3 Replies

2. Shell Programming and Scripting

How to print 1st field and last 2 fields together and the rest of the fields after it using awk?

Hi experts, I need to print the first field first then last two fields should come next and then i need to print rest of the fields. Input : a1,abc,jsd,fhf,fkk,b1,b2 a2,acb,dfg,ghj,b3,c4 a3,djf,wdjg,fkg,dff,ggk,d4,d5 Expected output: a1,b1,b2,abc,jsd,fhf,fkk... (6 Replies)
Discussion started by: 100bees
6 Replies

3. Shell Programming and Scripting

awk to match keyword and return matches and unique fields

Trying to use awk to find a keyword and return the matches in the row, but also $1 and $2, which are the unique id's, but they only appear once. Thank you :). file name 31 Index Chromosomal Position Gene Inheritance 122 2106725 TSC2 AD 124 2115481 TSC2 AD 121 2105400 TSC2 AD... (6 Replies)
Discussion started by: cmccabe
6 Replies

4. Shell Programming and Scripting

awk to combine by field and average by another

In the below awk I am trying to combine all matching $4 into a single $5 (up to the -), and count the lines in $6 and average all values in $7. The awk is close but it seems to only be using the last line in the file and skipping all others. The posted input is a sample of the file that is over... (3 Replies)
Discussion started by: cmccabe
3 Replies

5. Shell Programming and Scripting

awk to combine all matching fields in input but only print line with largest value in specific field

In the below I am trying to use awk to match all the $13 values in input, which is tab-delimited, that are in $1 of gene which is just a single column of text. However only the line with the greatest $9 value in input needs to be printed. So in the example below all the MECP2 and LTBP1... (0 Replies)
Discussion started by: cmccabe
0 Replies

6. Shell Programming and Scripting

awk to adjust coordinates in field based on sequential numbers in another field

I am trying to output a tab-delimited result that uses the data from a tab-delimited file to combine and subtract specific lines. If $4 matches in each line then the first matching sequential $6 value is added to $2, unless the value is 1, then the original $2 is used (like in the case of line... (3 Replies)
Discussion started by: cmccabe
3 Replies

7. Shell Programming and Scripting

awk to format file and combine two fields using comma

I am trying to use awk to format the file below, which is tab-delimited. The desired out is space delimited and is in the order of $9 $13 $2 $10-$11.$10 and $11 are often times multiple values separated by a comma, so the value in $10 is combined with the first value from $11 using the comma.... (5 Replies)
Discussion started by: cmccabe
5 Replies

8. Shell Programming and Scripting

awk to adjust text and count based on value in field

The below awk executes as is and produces the current output. It isvery close but what Ican not seem to do is add the -exon..., the ... portion comes from $1 and the _exon is static and will never change. If there is + sign in $4 then the ... is in acending order or sequential. If there is a - in... (2 Replies)
Discussion started by: cmccabe
2 Replies

9. UNIX for Beginners Questions & Answers

find pattern matches in consecutive lines in certain fields-awk

I have a text file with many thousands of lines, a small sample of which looks like this: InputFile:PS002,003 D -1 5 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 6 6 -1 -1 -1 -1 0 509 0 PS002,003 PSQ 0 1 7 18 1 0 -1 1 1 3 -1 -1 ... (5 Replies)
Discussion started by: jvoot
5 Replies

10. Shell Programming and Scripting

Perl to adjust coordinates based on repeat string

In the file below I am trying to count the given repeats of A,T,C,G in each string of letters. Each sequence is below the > and it is possible for a string of repeats to wrap from the line above. For example, in the first line the last letter is a T and the next lines has 3 more. I think the below... (10 Replies)
Discussion started by: cmccabe
10 Replies

LEARN ABOUT CENTOS

locale::codes::langext

Locale::Codes::LangExt(3)				User Contributed Perl Documentation				 Locale::Codes::LangExt(3)

NAME

       Locale::Codes::LangExt - standard codes for language extension identification

SYNOPSIS

	  use Locale::Codes::LangExt;

	  $lext = code2langext('acm');		       # $lext gets 'Mesopotamian Arabic'
	  $code = langext2code('Mesopotamian Arabic'); # $code gets 'acm'

	  @codes   = all_langext_codes();
	  @names   = all_langext_names();

DESCRIPTION

       The "Locale::Codes::LangExt" module provides access to standard codes used for identifying language extensions, such as those as defined in
       the IANA language registry.

       Most of the routines take an optional additional argument which specifies the code set to use. If not specified, the default IANA language
       registry codes will be used.

SUPPORTED CODE SETS

       There are several different code sets you can use for identifying language extensions. A code set may be specified using either a name, or
       a constant that is automatically exported by this module.

       For example, the two are equivalent:

	  $lext = code2langext('acm','alpha');
	  $lext = code2langext('acm',LOCALE_LANGEXT_ALPHA);

       The codesets currently supported are:

       alpha
	   This is the set of three-letter (lowercase) codes from the IANA language registry, such as 'acm' for Mesopotamian Arabic.

	   This is the default code set.

ROUTINES

       code2langext ( CODE [,CODESET] )
       langext2code ( NAME [,CODESET] )
       langext_code2code ( CODE ,CODESET ,CODESET2 )
       all_langext_codes ( [CODESET] )
       all_langext_names ( [CODESET] )
       Locale::Codes::LangExt::rename_langext  ( CODE ,NEW_NAME [,CODESET] )
       Locale::Codes::LangExt::add_langext  ( CODE ,NAME [,CODESET] )
       Locale::Codes::LangExt::delete_langext  ( CODE [,CODESET] )
       Locale::Codes::LangExt::add_langext_alias  ( NAME ,NEW_NAME )
       Locale::Codes::LangExt::delete_langext_alias  ( NAME )
       Locale::Codes::LangExt::rename_langext_code  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangExt::add_langext_code_alias  ( CODE ,NEW_CODE [,CODESET] )
       Locale::Codes::LangExt::delete_langext_code_alias  ( CODE [,CODESET] )
	   These routines are all documented in the Locale::Codes::API man page.

SEE ALSO

       Locale::Codes
	   The Locale-Codes distribution.

       Locale::Codes::API
	   The list of functions supported by this module.

       http://www.iana.org/assignments/language-subtag-registry
	   The IANA language subtag registry.

AUTHOR

       See Locale::Codes for full author history.

       Currently maintained by Sullivan Beck (sbeck@cpan.org).

COPYRIGHT

	  Copyright (c) 2011-2013 Sullivan Beck

       This module is free software; you can redistribute it and/or modify it under the same terms as Perl itself.

perl v5.16.3							    2013-02-27						 Locale::Codes::LangExt(3)
All times are GMT -4. The time now is 10:22 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy