Sponsored Content
Full Discussion: sort split merge -u unique
Top Forums Shell Programming and Scripting sort split merge -u unique Post 302551799 by jbr950 on Wednesday 31st of August 2011 04:54:56 PM
Old 08-31-2011
sort split merge -u unique

Hi, this is about sorting a very large file (like 10 gb) to keep lines with unique entries across SOME of the columns.

The line originally looked like this:

Code:
sort -u -k2,2 -k3,3n -k4,4n -k5,5n -k6,6n file_unsorted > file_sorted

please note the -u flag.

The problem is that this single command is taking more than 12 hours with 10 g of memory and I am looking for a way to speed things up.

I have heard that splitting a large file into subfiles, then sorting each subfile and then merging back together with the sort command can work, but I am imaging this will not work because I'm using the -u flag to keep only unique rows.

maybe split and then sort first WITHOUT the -u flag and then sort -m -u -k2,2 -k3,3n -k4,4n -k5,5n -k6,6n subfiles ?

I'm thinking of ways to test that, but please let me know if you have any ideas for me!

Thank you kindly.

Jonathan

Last edited by radoulov; 08-31-2011 at 06:01 PM.. Reason: Please use code tags for code and data samples, thank you
 

9 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

Sort and Unique in Perl

Hi, May I know, if a pipe separated File is large, what is the best method to calculate the unique row count of 3rd column and get a list of unique value of the 3rdcolum? Thanks in advance! (20 Replies)
Discussion started by: deepakwins
20 Replies

2. UNIX for Dummies Questions & Answers

split a file with unique sets

This may sound like a trivial problem, but I still need some help: I have a file with ids and I want to split it 'n' ways (could be any number) into files: 1 1 1 2 2 3 3 4 5 5 Let's assume 'n' is 3, and we cannot have the same id in two different partitions. So the partitions may... (8 Replies)
Discussion started by: ChicagoBlues
8 Replies

3. Shell Programming and Scripting

Awk sort and unique

Input file --------- 12:name1:|host1|host1|host2|host1 13:name2:|host1|host1|host2|host3 14:name3: ...... Required output --------------- 12:name1:host1(2)|host1(1) 13:name2:host1(2)|host2(1)|host3(1) 14:name3: where (x) - Count how many times field appears in last column ... (3 Replies)
Discussion started by: greycells
3 Replies

4. Shell Programming and Scripting

How to merge columns into lines, using unique keys?

I would really appreciate a sulution for this : invoice# client# 5929 231 4358 231 2185 231 6234 231 1166 464 1264 464 3432 464 1720 464 9747 464 1133 791 4930 791 5496 791 6291 791 8681 989 3023 989 (2 Replies)
Discussion started by: hemo21
2 Replies

5. UNIX for Dummies Questions & Answers

How to count specific columns and merge with unique ones?

Hi. I am not sure the title gives an optimal description of what I want to do. I have several text files that contain data in many columns. All the files are organized the same way, but the data in the columns might differ. I want to count the number of times data occur in specific columns,... (0 Replies)
Discussion started by: JamesT
0 Replies

6. UNIX for Dummies Questions & Answers

Print unique lines without sort or unique

I would like to print unique lines without sort or unique. Unfortunately the server I am working on does not have sort or unique. I have not been able to contact the administrator of the server to ask him to add it for several weeks. (7 Replies)
Discussion started by: cokedude
7 Replies

7. Shell Programming and Scripting

How to merge two files with unique values matching.?

I have one script as below: #!/bin/ksh Outputfile1="/home/OutputFile1.xls" Outputfile2="/home/OutputFile2.xls" InputFile1="/home/InputFile1.sql" InputFile2="/home/InputFile2.sql" echo "Select hobby, class, subject, sports, rollNumber from Student_Table" >> InputFile1 echo "Select rollNumber... (3 Replies)
Discussion started by: Sharma331
3 Replies

8. Shell Programming and Scripting

Sort unique

Hi, I have an input file that I have sorted in a previous stage by $1 and $4. I now need something that will take the first record from each group of data based on the key being $1 Input file 1000AAA|"ZZZ"|"Date"|"1"|"Y"|"ABC"|""|AA 1000AAA|"ZZZ"|"Date"|"2"|"Y"|"ABC"|""|AA... (2 Replies)
Discussion started by: Ads89
2 Replies

9. UNIX for Beginners Questions & Answers

Merge 4 bim files by keeping only the overlapping variants (unique rs values )

Dear community, I am facing a problem and I kindly ask your help: I have 4 different data sets consisted from 3 different types of array. On each file, column 1 is chromosome position, column 2 is SNP id etc... Lets say I have the following (bim) datasets: x2014: 1 rs3094315... (4 Replies)
Discussion started by: fondan
4 Replies
lsort(n)						       Tcl Built-In Commands							  lsort(n)

__________________________________________________________________________________________________________________________________________________

NAME
lsort - Sort the elements of a list SYNOPSIS
lsort ?options? list _________________________________________________________________ DESCRIPTION
This command sorts the elements of list, returning a new list in sorted order. The implementation of the lsort command uses the merge-sort algorithm which is a stable sort that has O(n log n) performance characteristics. By default ASCII sorting is used with the result returned in increasing order. However, any of the following options may be specified before list to control the sorting process (unique abbreviations are accepted): -ascii Use string comparison with Unicode code-point collation order (the name is for backward-compatability reasons.) This is the default. -dictionary Use dictionary-style comparison. This is the same as -ascii except (a) case is ignored except as a tie-breaker and (b) if two strings contain embedded numbers, the numbers compare as integers, not characters. For example, in -dictionary mode, bigBoy sorts between bigbang and bigboy, and x10y sorts between x9y and x11y. -integer Convert list elements to integers and use integer comparison. -real Convert list elements to floating-point values and use floating comparison. -command command Use command as a comparison command. To compare two elements, evaluate a Tcl script consisting of command with the two elements appended as additional arguments. The script should return an integer less than, equal to, or greater than zero if the first element is to be considered less than, equal to, or greater than the second, respectively. -increasing Sort the list in increasing order (``smallest'' items first). This is the default. -decreasing Sort the list in decreasing order (``largest'' items first). -index index If this option is specified, each of the elements of list must itself be a proper Tcl sublist. Instead of sorting based on whole sublists, lsort will extract the index'th element from each sublist and sort based on the given element. The keyword end is allowed for the index to sort on the last sublist element, and end-index sorts on a sublist element | offset from the end. For example, lsort -integer -index 1 {{First 24} {Second 18} {Third 30}} returns {Second 18} {First 24} {Third 30}, and | lsort -index end-1 {{a 1 e i} {b 2 3 f g} {c 4 5 6 d h}} | returns {c 4 5 6 d h} {a 1 e i} {b 2 3 f g}. This option is much more efficient than using -command to achieve the same effect. -unique If this option is specified, then only the last set of duplicate elements found in the list will be retained. Note that duplicates are determined relative to the comparison used in the sort. Thus if -index 0 is used, {1 a} and {1 b} would be considered duplicates and only the second element, {1 b}, would be retained. NOTES
The options to lsort only control what sort of comparison is used, and do not necessarily constrain what the values themselves actually are. This distinction is only noticeable when the list to be sorted has fewer than two elements. The lsort command is reentrant, meaning it is safe to use as part of the implementation of a command used in the -command option. EXAMPLES
Sorting a list using ASCII sorting: % lsort {a10 B2 b1 a1 a2} B2 a1 a10 a2 b1 Sorting a list using Dictionary sorting: % lsort -dictionary {a10 B2 b1 a1 a2} a1 a2 a10 b1 B2 Sorting lists of integers: % lsort -integer {5 3 1 2 11 4} 1 2 3 4 5 11 % lsort -integer {1 2 0x5 7 0 4 -1} -1 0 1 2 4 0x5 7 Sorting lists of floating-point numbers: % lsort -real {5 3 1 2 11 4} 1 2 3 4 5 11 % lsort -real {.5 0.07e1 0.4 6e-1} 0.4 .5 6e-1 0.07e1 Sorting using indices: % # Note the space character before the c % lsort {{a 5} { c 3} {b 4} {e 1} {d 2}} { c 3} {a 5} {b 4} {d 2} {e 1} % lsort -index 0 {{a 5} { c 3} {b 4} {e 1} {d 2}} {a 5} {b 4} { c 3} {d 2} {e 1} % lsort -index 1 {{a 5} { c 3} {b 4} {e 1} {d 2}} {e 1} {d 2} { c 3} {b 4} {a 5} Stripping duplicate values using sorting: % lsort -unique {a b c a b c a b c} a b c More complex sorting using a comparison function: % proc compare {a b} { set a0 [lindex $a 0] set b0 [lindex $b 0] if {$a0 < $b0} { return -1 } elseif {$a0 > $b0} { return 1 } return [string compare [lindex $a 1] [lindex $b 1]] } % lsort -command compare {{3 apple} {0x2 carrot} {1 dingo} {2 banana}} {1 dingo} {2 banana} {0x2 carrot} {3 apple} SEE ALSO
list(n), lappend(n), lindex(n), linsert(n), llength(n), lsearch(n), lset(n), lrange(n), lreplace(n) | KEYWORDS
element, list, order, sort Tcl 8.3 lsort(n)
All times are GMT -4. The time now is 03:58 PM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy