Login or Register to Ask a Question and Join Our Community

Sponsored Content
Full Discussion: Sorting a .csv using awk or other
Top Forums Shell Programming and Scripting Sorting a .csv using awk or other Post 302514962 by dunnybocter on Monday 18th of April 2011 03:03:56 PM
Old 04-18-2011
Sorting a .csv using awk or other
Hello all, I am new here and *relatively* new to Unix. I have a bit of an emergency. I have a three column file that I need to sort:

sample name, miRNA, reads per million (RPM)

There are multiple samples, and for each sample name there are multiple miRNAs and associated RPMs. Some of these miRNAs overlap between samples, but not all, so here is what the input file looks like

Sample 1, mirna1,RPM
Sample 1, mirna3,RPM
Sample 1, mirna4, RPM
Sample 2, mirna2,RPM
Sample2, mirna3, RPM
Sample2, mirna4, RPM

I need an output file that looks like this
miRNA1 miRNA2 .... miRNAx
Sample 1 RPM RPM
Sample 2 RPM RPM
Sample 3 RPM RPM
etc


Basically, each row should be a sample and each column should have the RPM corresponding the the miRNA for that sample. I also need to put a zero if there is no value for an miRNA in a specific sample. The output should be csv as well.

Any ideas or help would be greatly appreciated. I am trying to use awk but I'm lost and very much in a rush. MOST SINCERE THANKS IN ADVANCE!
 

10 More Discussions You Might Find Interesting

1. Shell Programming and Scripting

awk sorting

Hi, I have used the following code to sort two sets of data: awk '{printf "%10s %s\n",$1,$2}' The first column is text and the second involves numbers. I was just wondering how i would go about sorting the second number so that they ascend from the top? Thanks for any help (4 Replies)
Discussion started by: Jaken
4 Replies

2. Shell Programming and Scripting

Help sorting .csv file

Hi, I have a .csv file which contains script names, subjects and email_addresses The first two colums are always script name and subject, the next 20 colums are email address.. What i want to do is sort the email address in alphabetical order for each row and there's around 1200 rows. So... (3 Replies)
Discussion started by: Jazmania
3 Replies

3. Shell Programming and Scripting

sorting csv file based on column selected

Hi all, in my csv file it'll look like this, and of course it may have more columns US to UK;abc-hq-jcl;multimedia UK to CN;def-ny-jkl;standard DE to DM;abc-ab-klm;critical FD to YM;la-yr-tym;standard HY to MC;la-yr-ytm;multimedia GT to KJ;def-ny-jrt;critical I would like to group... (4 Replies)
Discussion started by: tententen
4 Replies

4. UNIX and Linux Applications

UNIX sorting - csv file

Hi, Please help me to solve sorting in CSV file. I have 25 columns in my CSV. (Delimiter is ",") Summary columns are from 10 to 13 which are should not be sorted. From 1-9 and 14-25 should be able to sort in ascending. how should i do this using Sort command in unix. If no simple commands pls... (0 Replies)
Discussion started by: rajani_p
0 Replies

5. Shell Programming and Scripting

Need help in writing a routine for sorting a CSV file

Hi, I have a CSV file in following manner: server1,env1,patch1 server1,env1,patch2 server1,env1,patch3 server1,env2,patch1 server1,env2,patch3 server2,env3,patch1 server2,env3,patch5 server2,env4,patch1 server3,env6,patch1 server3,env7,patch2 server3,env7,patch3 I want to... (6 Replies)
Discussion started by: avikaljain
6 Replies

6. Shell Programming and Scripting

CSV to SQL insert: Awk for strings with multiple lines in csv

Hi Fellows, I have been struggling to fix an issue in csv records to compose sql statements and have been really losing sleep over it. Here is the problem: I have csv files in the following pipe-delimited format: Column1|Column2|Column3|Column4|NEWLINE Address Type|some descriptive... (4 Replies)
Discussion started by: khayal
4 Replies

7. Shell Programming and Scripting

awk read column csv and search in other csv

hi, someone to know how can i read a specific column of csv file and search the value in other csv columns if exist the value in the second csv copy entire row with all field in a new csv file. i suppose that its possible using awk but i m not expertise thanks in advance (8 Replies)
Discussion started by: giankan
8 Replies

8. Shell Programming and Scripting

CSV Sorting on only particular columns

Hello! So ive been presented with this comma-delimited file: I need a print to look as below " lastname, phone_number, zip for every person with a last name starting with the letter H, I only with a 650-area code phone number. output should be sorted by reverse ZIP code " I only have... (5 Replies)
Discussion started by: strangemachine
5 Replies

9. Shell Programming and Scripting

Sorting the csv file in Perl

Hi All How all are doing today. Just struck in an issue in Perl I have a csv file which contain 32 column, I want to make sorting in that csv file with respect to 26th column. Is it possible to do so without any module being added? Regards Aditya ---------- Post updated at 10:02 AM... (11 Replies)
Discussion started by: adisky123
11 Replies

10. Shell Programming and Scripting

Sorting a CSV file by DOB

I have absolutaly no idea how to get this script to sort the info in Birthdays.csv by date of birth. I know the sort -n command, however i wish to sort the file birthdays.csv by DOB. How would i go about doing this? The below script gets user info and date of birth and then puts these info a... (3 Replies)
Discussion started by: redshine6
3 Replies

LEARN ABOUT DEBIAN

rec2csv

REC2CSV(1)							   User Commands							REC2CSV(1)

NAME

       rec2csv - rec to csv converter

SYNOPSIS

       rec2csv [OPTIONS]... [REC_FILE]

DESCRIPTION

       Convert rec data into csv data.

       -t, --type=TYPE
	      record set to convert to csv; if this parameter is omitted then the default record set is used

       -S, --sort=FIELD
	      sort the output by the specified field.

       --help print a help message and exit.

       --version
	      show version and exit.

AUTHOR

       Written by Jose E. Marchesi.

REPORTING BUGS

       Report bugs to: bug-recutils@gnu.org
       GNU recutils home page: <http://www.gnu.org/software/recutils/>
       General help using GNU software: <http://www.gnu.org/gethelp/>

COPYRIGHT

       Copyright (C) 2010, 2011, 2012 Jose E. Marchesi.  License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>.
       This is free software: you are free to change and redistribute it.  There is NO WARRANTY, to the extent permitted by law.

SEE ALSO

       The  full  documentation  for  rec2csv  is maintained as a Texinfo manual.  If the info and rec2csv programs are properly installed at your
       site, the command

	      info rec2csv

       should give you access to the complete manual.

rec2csv 1.4.93							   January 2012 							REC2CSV(1)
All times are GMT -4. The time now is 01:57 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy