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!
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LEARN ABOUT DEBIAN
dtc_install_centos
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)