Sponsored Content
Top Forums UNIX for Dummies Questions & Answers optimizing - to find the number of occurrence Post 302293552 by e3r1ck_ETT on Tuesday 3rd of March 2009 09:56:22 AM
Old 03-03-2009
I found the unix command to be useful.

cat filename | sort | uniq -c | sort -nr

What if I am using a tab-delimited text file with multiple columns?

Example:

S100A16 hsa-miR-125a-3p S100A16 0.0011959 0.768059
PBXIP1 hsa-miR-125a-3p PBXIP1 0.0199898 0.700326
CYB5R3 hsa-miR-125a-3p CYB5R3 0.0081174 0.748953
BEST3 hsa-miR-125a-3p BEST3 0.00148927 0.756234
FAM101A hsa-miR-125a-3p FAM101A 0.0196212 0.783555
KIAA0195 hsa-miR-125a-3p KIAA0195 0.0019755 0.747427
LLGL2 hsa-miR-125a-3p LLGL2 0.0248212 0.876563
FBLN5 hsa-miR-125a-3p FBLN5 0.0162988 0.776446
IFITM3 hsa-miR-125a-3p IFITM3 0.00896808 0.478704
SSH3 hsa-miR-125a-3p SSH3 0.0301693 0.836054
EXTERNAL_NAME SEQ EXTERNAL_NAME p-value(1 vs. 2) Ratio(1 vs. 2)
EMILIN1 hsa-miR-369-5p EMILIN1 0.0254294 0.720094
ADD3 hsa-miR-369-5p ADD3 0.0184075 0.742096
AIFM2 hsa-miR-369-5p AIFM2 0.00646348 0.829228
GPT2 hsa-miR-369-5p GPT2 0.00473291 0.706895

and I want the output to read

10 hsa-miR-125a-3p
4 hsa-miR-369-5p
1 SEQ

Initially, I made a new file, composing only the column of interest, using perl (column 1 here), named it filenam_list; then applied the

cat filenam_list | sort | uniq -c | sort -nr > filename_counts
rm filenam_list

Is there a more efficient way of doing this? I'm sure there has to be. I repeated the procedure on 7 files and I have to it again.
 

10 More Discussions You Might Find Interesting

1. UNIX for Dummies Questions & Answers

Line number of an occurrence using grep

Hi All, is there a way to extract the line number of an occurrence using grep? I know that with the -n option it prints out the line number as well. I would like to assign the line number to a variable. Thanks, Sarah (5 Replies)
Discussion started by: f_o_555
5 Replies

2. UNIX for Dummies Questions & Answers

line number of the i-th occurrence of a pattern

Hi all, is there a simple way to obtain the line number of the i-th occurrence of a pattern? I have OCCURRENCE=`grep -io "${STRING_NAME}" ${1}-${8}${EXT}.out_bis| wc -l` which tells me how many occurency I have. I would like to go through them and determine the line number and assign... (6 Replies)
Discussion started by: f_o_555
6 Replies

3. Shell Programming and Scripting

Uniq adresses with number of occurrence

Alo I have a file with a lot of addresses where I want to list unique addresses and the number of theirs occurrence. I have this input file: 0011bd09 ea 01 0b 04 ea 01 0b 38-bd 11 00 98 15 cb 01 00 .......8........ 0011bd09 ea 11 00 98 15 cb 01 00-00 00 00 d8 3d 8d 01 94 ... (5 Replies)
Discussion started by: chitech
5 Replies

4. Shell Programming and Scripting

find string nth occurrence in file and print line number

Hi I have requirement to find nth occurrence in a file and capture data from with in lines (between lines) Data in File. <QUOTE> <SESSION> <ATTRIBUTE NAME='Parameter Filename' VALUE='file1.parm'/> <ATTRIBUTE NAME='Service Name' VALUE='None'/> </SESSION> <SESSION> <ATTRIBUTE... (6 Replies)
Discussion started by: tmalik79
6 Replies

5. Shell Programming and Scripting

Count number of occurrence at each line

Hi I have the following file ENST001 ENST002 4 4 4 88 9 9 ENST004 3 3 3 99 8 8 ENST009 ENST010 ENST006 8 8 8 77 8 8 Basically I want to count how many times ENST* is repeated in each line so the expected results is 2 1 3 Any suggestion please ? (4 Replies)
Discussion started by: fuad_
4 Replies

6. Shell Programming and Scripting

number of occurrence

: i need a bash script to convert the displayed output 12 14 15 12 15 13 to 12 * 2 ,13 * 1,14*1,15*1 Thanks, nevil (2 Replies)
Discussion started by: nevil
2 Replies

7. Shell Programming and Scripting

How to count the occurrence of a number?

Hi, I have a file which contained a set of numbers like Col1 col2 col3 col4 1 sa 13 0 2 sb 14 0 3 sc 15 9 4 sd 16 -9 5 sd 20 -2 6 sd 20 4 Here in last column I need to count the zeros, positive values and negative values, please help me to do that. (2 Replies)
Discussion started by: Shenbaga.d
2 Replies

8. Shell Programming and Scripting

awk to find the number of occurrence

My file contains like this on 10 th line NM1*IL*1* awk '/NM1/{print NR}' *.dat output is 10 awk '/NM1*IL*1*/{print NR}' *.dat output is Nothing but im expecting 10 on second code as well . (4 Replies)
Discussion started by: Rajesh_us
4 Replies

9. Shell Programming and Scripting

awk or other way to find out number of occurrence of 7th character

Hi all, I am looking for to filter out based on 7th character and list the number of occurrence based on the 7th character if p , d , o or m 1. if 7th character is p , Output should be: p_hosts = N 2. if 7th character is d , Output should be: d_hosts = N 3. if 7th character is o , Output... (10 Replies)
Discussion started by: rveri
10 Replies

10. Shell Programming and Scripting

Optimizing find with many replacements

Hello, I'm looking for advice on how to optimize this bash script, currently i use the shotgun approach to avoid file io/buffering problems of forks trying to write simultaneously to the same file. i'd like to keep this as a fairly portable bash script rather than writing a C routine. in a... (8 Replies)
Discussion started by: f77hack
8 Replies
XPath::NodeSet(3pm)					User Contributed Perl Documentation				       XPath::NodeSet(3pm)

NAME
XML::XPath::NodeSet - a list of XML document nodes DESCRIPTION
An XML::XPath::NodeSet object contains an ordered list of nodes. The nodes each take the same format as described in XML::XPath::XMLParser. SYNOPSIS
my $results = $xp->find('//someelement'); if (!$results->isa('XML::XPath::NodeSet')) { print "Found $results "; exit; } foreach my $context ($results->get_nodelist) { my $newresults = $xp->find('./other/element', $context); ... } API
new() You will almost never have to create a new NodeSet object, as it is all done for you by XPath. get_nodelist() Returns a list of nodes. See XML::XPath::XMLParser for the format of the nodes. string_value() Returns the string-value of the first node in the list. See the XPath specification for what "string-value" means. to_literal() Returns the concatenation of all the string-values of all the nodes in the list. get_node($pos) Returns the node at $pos. The node position in XPath is based at 1, not 0. size() Returns the number of nodes in the NodeSet. pop() Equivalent to perl's pop function. push(@nodes) Equivalent to perl's push function. append($nodeset) Given a nodeset, appends the list of nodes in $nodeset to the end of the current list. shift() Equivalent to perl's shift function. unshift(@nodes) Equivalent to perl's unshift function. prepend($nodeset) Given a nodeset, prepends the list of nodes in $nodeset to the front of the current list. perl v5.10.1 2002-09-02 XPath::NodeSet(3pm)
All times are GMT -4. The time now is 10:10 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy