Sponsored Content
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
dtc_install_centos(8)					      System Manager's Manual					     dtc_install_centos(8)

NAME
dtc_install_centos - bootstrap a CentOS install to use in a chroot or VM SYNOPSIS
dtc_install_centos <install root> <yum environment> DESCRIPTION
This shell script is part of the dtc-xen package, generally to be used by the dtc panel to install a new a Xen VPS server. This script is called by dtc_reinstall_os when the user chooses to install the CentOS operating system. How it works: it generates a temporary yum configuration in the yum environment directory, that directs yum to act inside the install root instead of in the base system; then it kindly requests yum to install the basesystem, centos-release and yum packages onto it. Yum then uses the configuration to download the required (usually, security-updated) packages and then perform the RPM installation process under the install root. It requires both RPM and yum. It does work under Debian (it was developed in Ubuntu first). It should also work on RPM-based systems without destroying the system-wide RPM and yum configurations. OPTION
<install root> Target directory where CentOS will be deployed. Must exist beforehand. <yum environment> Directory where yum will store the repository manifests and configuration. Will be automatically created. Cached RPMs and manifests will be left, as usual, in a directory var/cache/yum inside the install root. EXAMPLE
dtc_install_centos /root/yum /xen/13 This will setup the operating system in /xen/13, with the CentOS configuration folder in /root/yum. BUGS
It's limited to CentOS 5 at the moment. It must be run as root. Under some circumstances, the installation process itself may kill processes running on the host machine. The chroot yum does should be sufficient to avoid this, but we haven't been able, yet, to ascertain why this fails sometimes. SEE ALSO
dtc_reinstall_os(8) VERSION
This documentation describes dtc_install_os version 0.3.1. See http://www.gplhost.com/software-dtc-xen.html for updates. dtc_install_centos(8)
All times are GMT -4. The time now is 03:40 AM.
Unix & Linux Forums Content Copyright 1993-2022. All Rights Reserved.
Privacy Policy