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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!
 

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scap-as-rpm(8)						  System Administration Utilities					    scap-as-rpm(8)

NAME
scap-as-rpm - manual page for scap-as-rpm DESCRIPTION
usage: scap-as-rpm [-h] [--pkg-name PKG_NAME] [--pkg-version PKG_VERSION] [--pkg-release PKG_RELEASE] [--pkg-summary PKG_SUMMARY] [--pkg-license PKG_LICENSE] [--pkg-scap-location PKG_SCAP_LOCATION] [--rpm-destination RPM_DESTINATION] [--srpm-destination SRPM_DESTINATION] FILE [FILE ...] Takes given SCAP input(s) and makes an RPM package that contains them. The result RPM can be installed using # yum install ./pack- age-name-1-1.rpm which will put the contents into /usr/share/xml/scap. No dependency on openscap or scapworkbench is enforced in the output package so you can use any SCAP-capable scanner to evaluate the content. positional arguments: FILE List of files that should be put into the result package. These should be SCAP XML files but such requirement is not enforced. optional arguments: -h, --help show this help message and exit --pkg-name PKG_NAME Name of the RPM package, if none is provided the basename of the first SCAP input is used. Ex.: xyzsecurity-guide --pkg-version PKG_VERSION --pkg-release PKG_RELEASE --pkg-summary PKG_SUMMARY Optional short description of the package. --pkg-license PKG_LICENSE Short name of the license that you want to publish the package under. Ex.: GPLv2+, BSD, ... --pkg-scap-location PKG_SCAP_LOCATION Folder where SCAP files are supposed to be installed. Each package will have its own folder inside this folder. RPM variables can be used and will be expanded as usual. It is recommended to keep the default settings. --rpm-destination RPM_DESTINATION The folder (absolute or relative to CWD) where the result RPM shall be saved. --srpm-destination SRPM_DESTINATION The folder (absolute or relative to CWD) where the result SRPM shall be saved. scap-as-rpm November 2013 scap-as-rpm(8)
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