Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Bash: join 2 files
Top Forums Shell Programming and Scripting Bash: join 2 files Post 302886417 by MumuGB on Friday 31st of January 2014 10:10:56 AM
Old 01-31-2014
Wrench Bash: join 2 files
Hello !

I want to join 2 files.
They look like this:
Code:
KE340296.1    1    0/0:11
KE340296.1    2    0/0:12
KE340296.1    6    0/1:13
KE340297.1    1    0/1:14
KE340297.1    3    0/1:15
KE340297.1    4    0/1:16

and
Code:
KE340296.1    1    0/0:21
KE340296.1    2    0/0:22
KE340296.1    3    0/1:23
KE340297.1    1    0/1:24
KE340297.1    2    0/1:25
KE340297.1    3    0/1:26

I would like to obtain this: Columns 1 and 2 are the two first columns of the two files. Column 3 corresponds to file1:col3 and column 4 to file2:col3.
Code:
KE340296.1    1    0/0:11   0/0:21
KE340296.1    2    0/0:12   0/0:22
KE340296.1    3    .        0/1:23
KE340296.1    6    0/1:13   .
KE340297.1    1    0/1:14   0/1:24
KE340297.1    2    .        0/1:25
KE340297.1    3    0/1:15   0/1:26
KE340297.1    4    0/1:16   .

Let me explain:
These two files are sorted by first the colum 1 where I have this names KE... and then by the column 2 (position).
The tricky thing is that for some position, I don't have a value in one of the file. For instance in KE340296.1, position 4, I have only a value in the first file.
The file I want to obtain contains all the positions represented in the two files (there may be hole, as for KE340296.1, no position 4 and 5 in either of the two files) and if there is no value for one of the file, then I would like a dot or whatever character.

I wanted to use "join" but it seems that it won't work because positions are not perfectly matching.

Any one knows how I can do that ?

Thanks a lot !

Mu
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

join files

Hi , I want to join 2 files based on 2 column join condition. a11 john 2230 5000 a12 XXX 2230 A B 200 345 Expected O/P John 2230 5000 A B 200 I have tried this awk 'NR==FNR{a=$1;next}a&&sub($1,a)' a11 a12 > a13 (3 Replies)
Discussion started by: mohan705
3 Replies

2. Shell Programming and Scripting

[bash] join command

Hi I've 2 files: I'd like to get an output like: if I do like: join file1 file2 I get Where line 30 miss. I'm reading this old post: https://www.unix.com/unix-dummies-questions-answers/14647-join-command.html. Where a solutionn with awk is suggested. I mean is possible get the same... (5 Replies)
Discussion started by: Dedalus
5 Replies

3. UNIX for Dummies Questions & Answers

Join 2 files with multiple columns: awk/grep/join?

Hello, My apologies if this has been posted elsewhere, I have had a look at several threads but I am still confused how to use these functions. I have two files, each with 5 columns: File A: (tab-delimited) PDB CHAIN Start End Fragment 1avq A 171 176 awyfan 1avq A 172 177 wyfany 1c7k A 2 7... (3 Replies)
Discussion started by: InfoSeeker
3 Replies

4. Shell Programming and Scripting

Bash join script not working

So i'm currently working on a project where I'm attempting to display information of users from the /etc/passwd file and also another information file holding addition information about users. Problem is I've been trying to join the two files together and have all of the information about each... (2 Replies)
Discussion started by: Nostyx
2 Replies

5. UNIX for Dummies Questions & Answers

how to join two files using "Join" command with one common field in this problem?

file1: Toronto:12439755:1076359:July 1, 1867:6 Quebec City:7560592:1542056:July 1, 1867:5 Halifax:938134:55284:July 1, 1867:4 Fredericton:751400:72908:July 1, 1867:3 Winnipeg:1170300:647797:July 15, 1870:7 Victoria:4168123:944735:July 20, 1871:10 Charlottetown:137900:5660:July 1, 1873:2... (2 Replies)
Discussion started by: mindfreak
2 Replies

6. UNIX for Dummies Questions & Answers

How to use the the join command to join multiple files by a common column

Hi, I have 20 tab delimited text files that have a common column (column 1). The files are named GSM1.txt through GSM20.txt. Each file has 3 columns (2 other columns in addition to the first common column). I want to write a script to join the files by the first common column so that in the... (5 Replies)
Discussion started by: evelibertine
5 Replies

7. Shell Programming and Scripting

How to join 2 text files using bash scripting?

Hi Guys, I want to combine 2 files and and put together in 1 file . See below desired output. Any help will be much appreciated. FILE AX 2134 101L 12345.00 22222.00 1 10 X 2134 101L 12345.00 22222.00 11 20 X 2134 101L 12345.00 22222.00 21 30 X 2134 111L 77777.00 ... (3 Replies)
Discussion started by: H.R
3 Replies

8. UNIX for Beginners Questions & Answers

BASH join command error PLS

i've tried every variation possible and keep getting not sorted error. can anyone shed any light on how to do this? (image attached) (1 Reply)
Discussion started by: deadcick
1 Replies

9. Shell Programming and Scripting

Join columns across multiple lines in a Text based on common column using BASH

Hello, I have a file with 2 columns ( tableName , ColumnName) delimited by a Pipe like below . File is sorted by ColumnName. Table1|Column1 Table2|Column1 Table5|Column1 Table3|Column2 Table2|Column2 Table4|Column3 Table2|Column3 Table2|Column4 Table5|Column4 Table2|Column5 From... (6 Replies)
Discussion started by: nv186000
6 Replies

10. Shell Programming and Scripting

Join, merge, fill NULL the void columns of multiples files like sql "LEFT JOIN" by using awk

Hello, This post is already here but want to do this with another way Merge multiples files with multiples duplicates keys by filling "NULL" the void columns for anothers joinning files file1.csv: 1|abc 1|def 2|ghi 2|jkl 3|mno 3|pqr file2.csv: 1|123|jojo 1|NULL|bibi... (2 Replies)
Discussion started by: yjacknewton
2 Replies

LEARN ABOUT MOJAVE

locale::codes::langext

Locale::Codes::LangExt(3pm)				 Perl Programmers Reference Guide			       Locale::Codes::LangExt(3pm)

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 v5.18.2							    2013-11-04					       Locale::Codes::LangExt(3pm)
All times are GMT -4. The time now is 03:32 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy