AWK Matching Fields and Combining Files


 
Thread Tools Search this Thread
Top Forums Shell Programming and Scripting AWK Matching Fields and Combining Files
Prev   Next
# 1  
Old 03-29-2009
AWK Matching Fields and Combining Files

Hello!

I am writing a program to run through two large lists of data (~300,000 rows), find where rows in one file match another, and combine them based on matching fields. Due to the large file sizes, I'm guessing AWK will be the most efficient way to do this. Overall, the input and output I'm looking for is similar to to this:

File1: *first three columns are coordinates in (x, y, z)*
123 456 678 A B C
234 345 567 D F B
234 456 324 H J K
765 432 987 M N K


File2: *the last three columns are coordinates in (x, y, z)*
45 234 345 567
46 765 432 987
47 111 222 333
48 234 345 567
49 987 765 432
50 444 555 666
51 765 432 987
... and so on

Output file:
45 234 345 567 D F B
46 765 432 987 M N K
48 234 345 567 D F B
51 765 432 987 M N K

File2 has many more entries than File1, and every coordinate in File1 is located somewhere in File2. The problem I am having is how to search through all of File2 finding where each of the individual File1 coordinates is listed, and the number in column 1 of File2 that corresponds to that coordinate.

In a nutshell:
Make new file3
Find where File2($2, $3, $4) is equal to File1($1, $2, $3)
print to file3 File2($1, $2, $3, $4), File1($4, $5, $6)

Thank you!
 
Login or Register to Ask a Question

Previous Thread | Next Thread

10 More Discussions You Might Find Interesting

1. UNIX for Beginners Questions & Answers

awk for matching fields between files with repeated records

Hello all, I am having trouble with what should be an easy task, but seem to be missing something fundamental. I have two files, with File 1 consisting of a single field of many thousands of records. I also have File 2 with two fields and many thousands of records. My goal is that when $1 of... (2 Replies)
Discussion started by: jvoot
2 Replies

2. UNIX for Beginners Questions & Answers

Continued trouble matching fields in different files and selective field printing ([g]awk)

I apologize in advance, but I continue to have trouble searching for matches between two files and then printing portions of each to output in awk and would very much appreciate some help. I have data as follows: File1 PS012,002 PRQ 0 1 1 17 1 0 -1 3 2 1 2 -1 ... (7 Replies)
Discussion started by: jvoot
7 Replies

3. Shell Programming and Scripting

awk to print fields that match using conditions and a default value for non-matching in two files

Trying to use awk to match the contents of each line in file1 with $5 in file2. Both files are tab-delimited and there may be a space or special character in the name being matched in file2, for example in file1 the name is BRCA1 but in file2 the name is BRCA 1 or in file1 name is BCR but in file2... (6 Replies)
Discussion started by: cmccabe
6 Replies

4. UNIX for Beginners Questions & Answers

Awk: matching multiple fields between 2 files

Hi, I have 2 tab-delimited input files as follows. file1.tab: green A apple red B apple file2.tab: apple - A;Z Objective: Return $1 of file1 if, . $1 of file2 matches $3 of file1 and, . any single element (separated by ";") in $3 of file2 is present in $2 of file1 In order to... (3 Replies)
Discussion started by: beca123456
3 Replies

5. Shell Programming and Scripting

Awk: adding fields after matching $1

Dear AWK-experts! I did get stuck in the task of combining files after matching fields, so I'm still awkward with learning AWK. There are 2 files: one containing 3 columns with ID, coding status, and score for long noncoding RNAs: file1 (1.txt) (>5000 lines) ... (12 Replies)
Discussion started by: kben
12 Replies

6. Shell Programming and Scripting

AWK- delimiting the strings and matching the fields

Hello, I am newbie in awk. I have just started learning it. 1) I have input file which looks like: {4812 4009 1602 2756 306} {4814 4010 1603 2757 309} {8116 9362 10779 } {10779 10121 9193 10963 10908} {1602 2756 306 957 1025} {1603 2757 307} and so on..... 2) In output: a)... (10 Replies)
Discussion started by: kajolo
10 Replies

7. Shell Programming and Scripting

To get an output by combining fields from two different files

Hi guys, I couldn't find solution to this problem. If anyone knows please help me out. your guidance is highly appretiated. I have two files - FILE1 has the following 7 columns ( - has been added to make columns visible enough else columns are separated by single space) 155.34 - leg - 1... (8 Replies)
Discussion started by: smriti_shridhar
8 Replies

8. Shell Programming and Scripting

Matching and combining two files

Hi there, I have two files. What I want to do is search for the values in second field of file1 in the 6th field of the file2 and of they match to add the fields 1-5 of the file2 at the end of the line of file1 with a comma before. E.g File1 FWB,CHUAGT87HUMAS/BUD01,REUAIR08KLM... (3 Replies)
Discussion started by: sickboy
3 Replies

9. Shell Programming and Scripting

combining fields in awk

I am using: ps -A -o command,%cpu to get process and cpu usage figures. I want to use awk to split up the columns it returns. If I use: awk '{print "Process: "$1"\nCPU Usage: "$NF"\n"}' the $NF will get me the value in the last column, but if there is more than one word in the... (2 Replies)
Discussion started by: json4639
2 Replies

10. Shell Programming and Scripting

Matching and combining two files

Hi, How can I match the first two fields of file2 against the first two fields of file1 and where they match combine the two lines. If the name (example-Aidan Rielly) is in file1 but not in file2 then just write the info from file1 to the combined output file. If the name (example-Silvia... (5 Replies)
Discussion started by: p3t3r
5 Replies
Login or Register to Ask a Question
CLUSTER(7)						  PostgreSQL 9.2.7 Documentation						CLUSTER(7)

NAME
CLUSTER - cluster a table according to an index SYNOPSIS
CLUSTER [VERBOSE] table_name [ USING index_name ] CLUSTER [VERBOSE] DESCRIPTION
CLUSTER instructs PostgreSQL to cluster the table specified by table_name based on the index specified by index_name. The index must already have been defined on table_name. When a table is clustered, it is physically reordered based on the index information. Clustering is a one-time operation: when the table is subsequently updated, the changes are not clustered. That is, no attempt is made to store new or updated rows according to their index order. (If one wishes, one can periodically recluster by issuing the command again. Also, setting the table's FILLFACTOR storage parameter to less than 100% can aid in preserving cluster ordering during updates, since updated rows are kept on the same page if enough space is available there.) When a table is clustered, PostgreSQL remembers which index it was clustered by. The form CLUSTER table_name reclusters the table using the same index as before. You can also use the CLUSTER or SET WITHOUT CLUSTER forms of ALTER TABLE (ALTER_TABLE(7)) to set the index to be used for future cluster operations, or to clear any previous setting. CLUSTER without any parameter reclusters all the previously-clustered tables in the current database that the calling user owns, or all such tables if called by a superuser. This form of CLUSTER cannot be executed inside a transaction block. When a table is being clustered, an ACCESS EXCLUSIVE lock is acquired on it. This prevents any other database operations (both reads and writes) from operating on the table until the CLUSTER is finished. PARAMETERS
table_name The name (possibly schema-qualified) of a table. index_name The name of an index. VERBOSE Prints a progress report as each table is clustered. NOTES
In cases where you are accessing single rows randomly within a table, the actual order of the data in the table is unimportant. However, if you tend to access some data more than others, and there is an index that groups them together, you will benefit from using CLUSTER. If you are requesting a range of indexed values from a table, or a single indexed value that has multiple rows that match, CLUSTER will help because once the index identifies the table page for the first row that matches, all other rows that match are probably already on the same table page, and so you save disk accesses and speed up the query. CLUSTER can re-sort the table using either an index scan on the specified index, or (if the index is a b-tree) a sequential scan followed by sorting. It will attempt to choose the method that will be faster, based on planner cost parameters and available statistical information. When an index scan is used, a temporary copy of the table is created that contains the table data in the index order. Temporary copies of each index on the table are created as well. Therefore, you need free space on disk at least equal to the sum of the table size and the index sizes. When a sequential scan and sort is used, a temporary sort file is also created, so that the peak temporary space requirement is as much as double the table size, plus the index sizes. This method is often faster than the index scan method, but if the disk space requirement is intolerable, you can disable this choice by temporarily setting enable_sort to off. It is advisable to set maintenance_work_mem to a reasonably large value (but not more than the amount of RAM you can dedicate to the CLUSTER operation) before clustering. Because the planner records statistics about the ordering of tables, it is advisable to run ANALYZE(7) on the newly clustered table. Otherwise, the planner might make poor choices of query plans. Because CLUSTER remembers which indexes are clustered, one can cluster the tables one wants clustered manually the first time, then set up a periodic maintenance script that executes CLUSTER without any parameters, so that the desired tables are periodically reclustered. EXAMPLES
Cluster the table employees on the basis of its index employees_ind: CLUSTER employees USING employees_ind; Cluster the employees table using the same index that was used before: CLUSTER employees; Cluster all tables in the database that have previously been clustered: CLUSTER; COMPATIBILITY
There is no CLUSTER statement in the SQL standard. The syntax CLUSTER index_name ON table_name is also supported for compatibility with pre-8.3 PostgreSQL versions. SEE ALSO
clusterdb(1) PostgreSQL 9.2.7 2014-02-17 CLUSTER(7)