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Full Discussion: Remove Duplicate Two Line Pairs?
Top Forums UNIX for Dummies Questions & Answers Remove Duplicate Two Line Pairs? Post 302772477 by bakere19 on Monday 25th of February 2013 08:52:51 PM
Old 02-25-2013
Remove Duplicate Two Line Pairs?
So I have a bunch of files that look like this
Code:
>gi|33332323
MMKCRGVIMVVEKVMKRDGRIVPFDESRIRWAVQ---
>gi|45235353
MMKCR----VEKMRDVFFDESIRWAVQ

They go on...sequences are much longer but all in two line (fasta) format.

I want to remove duplicate pairs of ID(GI) number and sequence. I tried using grep ">" to get all the header lines, then sort -u > uniquegilist. Then I wrote the loop
Code:
for x in `cat uniquegilist`; do grep -m 1 -A1 $x sequencefile;done

I'm not sure why it didn't work, but that just returned the list of unique GI numbers and didn't include the sequences.

Any ideas on how to grab the unique GI # and sequence together...preferably preserving format?
 

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LEARN ABOUT BSD

zgrep

ZGREP(1)						      General Commands Manual							  ZGREP(1)

NAME

       zgrep - search possibly compressed files for a regular expression

SYNOPSIS

       zgrep [ grep_options ] [ -e ] pattern filename...

DESCRIPTION

       Zgrep  invokes  grep  on  compressed  or  gzipped  files.   These  grep	options  will  cause  zgrep  to  terminate  with  an  error  code:
       (-[drRzZ]|--di*|--exc*|--inc*|--rec*|--nu*).  All other options specified are passed directly to grep.  If no file is specified,  then  the
       standard input is decompressed if necessary and fed to grep.  Otherwise the given files are uncompressed if necessary and fed to grep.

       If the GREP environment variable is set, zgrep uses it as the grep program to be invoked.

EXIT CODE

       2 - An option that is not supported was specified.

AUTHOR

       Charles Levert (charles@comm.polymtl.ca)

SEE ALSO

       grep(1), gzexe(1), gzip(1), zdiff(1), zforce(1), zmore(1), znew(1)

																	  ZGREP(1)
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