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Full Discussion: RNA-seq analysis
Top Forums UNIX for Dummies Questions & Answers RNA-seq analysis Post 302769266 by bakunin on Monday 11th of February 2013 06:17:33 PM
Old 02-11-2013
Quote:
Originally Posted by genGirl23
I have tried.... grep "IH:i:1" file.sam > filtered.sam

but this will also return "IH:i:11 IH:i:12" etc etc. I have also tried "IH:i:1 " which returns nothing (I believe it's tab delimited)
As you didn't post a sample of your file i am left to guessing, but no problem: just give me a moment while i inspect your file with my crystal ball....

OK, somehow the device must be broken, but i can still give you some pointers:

"grep" always searches for the expression you give it. "1" will find "1", but also "11", "12", "1blabla", etc.. The trick therefore is to make to expression longer, up to a point where all the wrong lines are excluded.

Having said this: if you are sure (instead of just guessing) that the expression is followed by a tab you could add this tab as part of the expression. grep accepts this, but you will have to enclose your expression in single quotes to protect it from the shell evaluation process. In the following "<TAB>" means a literal tab character:

Code:
grep 'IH:i:1<TAB>' /path/to/infile > filtered.file

You can verify the character following being a tab by opening the file in a "vi" editor and enter ":set list" to display all the non-printable characters. Tabs will be displayed as "^I".

In case you just don't want any digit to follow your expression you simply forbid that instead of trying to find out what follows your expression:

Code:
grep 'IH:i:1[^0-9]' /path/to/infile > filtered.file

"[^0-9]" means "any character except numbers 0-9". The "[...]" means "any one character inside" and the "^" at the beginning reverses the meaning.

I hope this helps.

bakunin
This User Gave Thanks to bakunin For This Post:
genGirl23
 

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LEARN ABOUT DEBIAN

bp_search2alnblocks

BP_SEARCH2ALNBLOCKS(1p) 				User Contributed Perl Documentation				   BP_SEARCH2ALNBLOCKS(1p)

NAME

       search2alnblocks - Turn SearchIO parseable reports(s) into a set of aligned blocks

SYNOPSIS

	 search2alnblocks --minid PERCENTID --minlen LEN --minevalue EVALUE file1.
	 blast file2.blast ...> out.fas

DESCRIPTION

       This script will parse and filter BLAST (or other formats Bio::SearchIO can parse) output and format the alignment as blocks of alignments
       based on the HSPs.  Note this can only work if the input file parsed contains the necessary.

       Typically this can be used to turn BLAST output into a FASTA alignment format for input into the QRNA comparative gene finder for RNA genes
       (E.Rivas).

OPTIONS

	--maxevalue   Maximum E-value for an HSP
	--minevalue   Minimum E-value for an HSP
	--minlen      Minimum length of an HSP [default 0]
	--maxid       Maximum Percent Id [default 100]
		      (to help remove sequences which are really close)
	--minid       Minimum Percent Identity for an HSP [default 0]
	-i/--input    An optional input filename (expects input on STDIN by default)
	-o/--output   An optional output filename (exports to STDOUT by default)
	-f/--format   Specify a different Search Alignment format-
		      {fasta, axt, waba, blast, blastxml} are all permitted
		      although the format must have actual alignment
		      sequence for this script to work
		      See L<Bio::SearchIO> for more information.
	-of/--outformat Output format for the alignment blocks, anything
		      L<Bio::AlignIO> supports.
	-v/--verbose  Turn on debugging

AUTHOR - Jason Stajich
       Jason Stajich, jason-at-bioperl-dot-org.

perl v5.14.2							    2012-03-02						   BP_SEARCH2ALNBLOCKS(1p)
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