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Top Forums Shell Programming and Scripting How can I remove those duplicate sequence in UNIX?What command line I should type? Post 302279496 by skar_a on Friday 23rd of January 2009 12:18:13 AM
Old 01-23-2009
Quote:
Originally Posted by patrick chia
Hi, fajohnson...
Your command line is worked. But still left all the header of the nucleotide sequence. Do you have better idea that I just remain the first header of those same nucleotide sequence?
My input:
>HWI-EAS382_30FC7AAXX:4:1:631:449
>HWI-EAS382_30FC7AAXX:4:1:93:1407
>HWI-EAS382_30FC7AAXX:4:1:154:1123
>HWI-EAS382_30FC7AAXX:4:1:912:1008
>HWI-EAS382_30FC7AAXX:4:1:57:316
>HWI-EAS382_30FC7AAXX:4:1:1287:1193
>HWI-EAS382_30FC7AAXX:4:1:1451:1559
>HWI-EAS382_30FC7AAXX:4:1:1431:1913
TTTCCGCGAACTGCAAAAGACGTTTCGTATGCCGTT

My output just want left this:
>HWI-EAS382_30FC7AAXX:4:1:631:449
TTTCCGCGAACTGCAAAAGACGTTTCGTATGCCGTT

Thanks for your advise. Have a nice day.
Try this:
Code:
awk '/^>/{if(hdr=="") hdr=$0}/^[^>]/{x[$0]++;if(x[$0]==1) {print hdr;print} hdr=""}' infile

 

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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: xmlstarlet <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)
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