01-20-2009
How to use the programming in UNIX to count the total G+C and the GC%?What command li
Seems like can use awk and perl command. But I don't have the idea to write the command line. Thanks for all of your advise.
For example, if I have the file whose content are:
Sample 1. ATAGCAGAGGGAGTGAAGAGGTGGTGGGAGGGAGCT
Sample 2. ACTTTTATTTGAATGTAATATTTGGGACAATTATTC
Sample 3. AAATCATGGTGGGTTTATTGATGGTTAGAAAGTTCC
All the sample above, got 36 nucleotide.
I want my output to count the G + C and GC %. So my output should look like this:
Sample 1: G+C = 21 GC%= 58.33%
Sample 2: G+C = 8 GC%=22.22%
Sample 3: G+C = 13 GC%=36.11%
Thanks and appreciate of your answer.
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LEARN ABOUT SUSE
xmlstarlet
XMLSTARLET(1) xmlstarlet Manual XMLSTARLET(1)
NAME
xmlstarlet - command line XML/XSLT toolkit
SYNOPSIS
xmlstarlet [<options>] [<command>] [<cmd-options>]
INTRODUCTION
XMLStarlet is a set of command line utilities (tools) which can be used to transform, query, validate, and edit XML documents and files us-
ing simple set of shell commands in similar way it is done for plain text files using UNIX grep, sed, awk, diff, patch, join, etc commands.
This set of command line utilities can be used by those who deal with many XML documents on UNIX shell command prompt as well as for auto-
mated XML processing with shell scripts.
OPTIONS
--version
Display the version of xmlstarlet.
--help Display help.
COMMANDS
Type: xml <command> --help <ENTER> for command help
Available commands include:
ed (or edit)
Edit/update XML document(s).
sel (or select)
Select data or query XML document(s) (XPATH, etc).
tr (or transform)
Transform XML documents(s) using XSLT.
val (or validate)
Validate XML document(s) (well-formed/DTD/XSD/RelaxNG).
fo (or format)
Format XML document(s).
el (or elements)
Display element structure of XML document.
c14n (or canonic)
XML canonicalization.
ls (or list)
List directory as XML.
esc (or escape)
Escape special XML characters.
unesc (or unescape)
Unescape special XML characters.
pyx (or xmln)
Convert XML into PYX format (based on ESIS - ISO 8879).
p2x (or depyx)
Convert PYX into XML.
REFERENCES
XMLStarlet is a command line toolkit to query/edit/check/transform XML documents (for more information see http://xmlstar.source-
forge.net/).
AUTHOR
Mikhail Grushinskiy.
XMLSTARLET(1)