Awk with Multiple files


 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting Awk with Multiple files
# 1  
Old 12-12-2011
Awk with Multiple files

Hello,

I wanted to know the best way to do some matching between two files. I am currently using awk.

Example Question: If column 4 from file A is contained in column 1 from file B. Print the whole row from file A of mix of information from both files. i.e.

File A
Code:
chr1	1104384	1104467	hsa-mir-429
chr1	21314806	21314925	hsa-mir-1256
chr1	23189651	23189719	hsa-mir-4253
chr1	28833876	28834083	U17a

File B
Code:
name              start end acc
"hsa-mir-429-5p"	6 27	"MIMAT0000062"
"hsa-mir-429-3p"	57 77	"MIMAT0004481"
"hsa-mir-4253"	5 26	"MIMAT0000062"
"hsa-mir-1256-3p"	50 71	"MIMAT0010195"

Output
Code:
chr1	1104384	1104467	hsa-mir-429  "hsa-mir-429-5p"	6 27	"MIMAT0000062"
chr1	1104384	1104467	hsa-mir-429 "hsa-mir-429-3p"	57 77	"MIMAT0004481"
chr1	21314806	21314925	hsa-mir-1256 "hsa-mir-1256-3p"	50 71	"MIMAT0010195"
chr1	23189651	23189719	hsa-mir-4253 "hsa-mir-4253"    5 26	"MIMAT0000062"

Moderator's Comments:
Mod Comment How to use code tags

Last edited by Franklin52; 12-13-2011 at 05:09 AM.. Reason: Please use code tags for code and data samples, thank you
# 2  
Old 12-12-2011
Code:
perl -lane 'open I,"<fileB";for(<I>){@x=split/\s+/,$_;($x[0]=~/$F[3]/)&&print "@F @x"};close I' fileA

Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk, multiple files input and multiple files output

Hi! I'm new in awk and I need some help. I have a folder with a lot of files and I need that awk do something in each file and print a new file with the output. The input file name should be modified when I print the outpu files. Thanks in advance for help! :-) ciao (5 Replies)
Discussion started by: gabrysfe
5 Replies

2. Shell Programming and Scripting

perform 3 awk commands to multiple files in multiple directories

Hi, I have a directory /home/datasets/ which contains a bunch (720) of subdirectories called hour_1/ hour_2/ etc..etc.. in each of these there is a single text file called (hour_1.txt in hour_1/ , hour_2.txt for hour_2/ etc..etc..) and i would like to do some text processing in them. Each of... (20 Replies)
Discussion started by: amarn
20 Replies

3. UNIX for Dummies Questions & Answers

awk in multiple files

Hello all, I have two files: one that looks like this string1 string2 string3 string6 and another that looks like this Wstring1 apple Wstring2 vegetable Wstring3 mouse Wstring4 (3 Replies)
Discussion started by: FelipeAd
3 Replies

4. UNIX for Dummies Questions & Answers

Using AWK: Extract data from multiple files and output to multiple new files

Hi, I'd like to process multiple files. For example: file1.txt file2.txt file3.txt Each file contains several lines of data. I want to extract a piece of data and output it to a new file. file1.txt ----> newfile1.txt file2.txt ----> newfile2.txt file3.txt ----> newfile3.txt Here is... (3 Replies)
Discussion started by: Liverpaul09
3 Replies

5. UNIX for Dummies Questions & Answers

best method of replacing multiple strings in multiple files - sed or awk? most simple preferred :)

Hi guys, say I have a few files in a directory (58 text files or somthing) each one contains mulitple strings that I wish to replace with other strings so in these 58 files I'm looking for say the following strings: JAM (replace with BUTTER) BREAD (replace with CRACKER) SCOOP (replace... (19 Replies)
Discussion started by: rich@ardz
19 Replies

6. Shell Programming and Scripting

extract multiple cloumns from multiple files; skip rows and include filenames; awk

Hello, I am trying to write a bash shell script that does the following: 1.Finds all *.txt files within my directory of interest 2. reads each of the files (25 files) one by one (tab-delimited format and have the same data format) 3. skips the first 10 rows of the file 4. extracts and... (4 Replies)
Discussion started by: manishabh
4 Replies

7. UNIX for Dummies Questions & Answers

awk multiple files

Hi there! I'm with a problem because I'm working on a script to do a calculation of a mean using multiple files with 3 columns and N-lines. My input are like this File1 0001 0023 5 0120 0376 6 0412 3412 3 ... File2 0001 0023 3 0120 0376 nan 0412 3412 7 ... (1 Reply)
Discussion started by: philstar
1 Replies

8. Shell Programming and Scripting

Multiple search string in multiple files using awk

Hi, filenames: contains name of list of files to search in. placelist contains the names of places to be searched in all files in "filenames" for i in $(<filenames) do egrep -f placelist $i if ] then echo $i fi done >> outputfile Output i am getting: (0 Replies)
Discussion started by: pinnacle
0 Replies

9. Shell Programming and Scripting

awk with multiple files

I have 2 files first is category: 1:Phone 2:Keyboard 3:Printer 4:Scanner 5:Mouse the second is product: 1:iphone:1:..... 2:blackberry:1:..... 3:Mitsumi:2:..... 4:abc:5:..... 5:def:4:..... 6:noi:3:..... which bold numbers are "foreign key" in product file and they are "primary... (5 Replies)
Discussion started by: WuZun
5 Replies

10. Shell Programming and Scripting

Splitting input files into multiple files through AWK command

Hi, I needs to split *.txt files from single directory depends on the some mutltiple input values. i have wrote the code like below for file in *.txt do grep -i -h "value1|value2" $file > $file; done. My requirment is more input values needs to be given in grep; let us say 50... (3 Replies)
Discussion started by: arund_01
3 Replies
Login or Register to Ask a Question

Featured Tech Videos