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Full Discussion: Piping with grep
Operating Systems Linux Ubuntu Piping with grep Post 302529400 by frymor on Thursday 9th of June 2011 09:10:17 AM
Old 06-09-2011
Piping with grep
Hi everybody,

I have a big file with blast results (if you know what this means, otherwise look at it just as a text file with a specific form).

I am trying to extract some ids from within this file, which have certain parameters.
For example, some Of my IDs have the term 'No hit results' connected to them.
This is what I am trying to extract.
this is how it looks loike:
Code:
Query= ssc-miR-345-3p_st

Length=21

RID: 1307544734-17235-35154543375.BLASTQ1

***** No hits found *****

Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 

Effective search space used: 0

In the complete file I have 15517 'Query=' and for 389 of them I can also find 'No hits found'.

My Qeustion is how can I found out which Queries are connected to this 'No hits'.

I tried it with :
Code:
split -a 5 -p '/Query=' filename

grep -lr 'No' . | grep 'Query='

But this doesn't work.

I just don't understand how to grep in many files and than pipe it to a second grep option.

I would be happy for any help.
Thanks

Assa
This User Gave Thanks to frymor For This Post:
 

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LEARN ABOUT LINUX

zegrep

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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