Shell – grep ignoring pipe when aliased to ‘grep -R’

aliasgreppipeshell

I'm trying to pipe the output of a grep search into the input of another grep.
Such as:

grep search_query * | grep -v but_not_this

But the second grep is not using the output of the previous search. It looks like the second grep is just using * instead. For example,

grep lcov *                                                                                          
tst/bits/Module.mk:21:$(call func_report_lcov)
tst/drivers/Module.mk:27:$(call func_report_lcov)

But when I want to filter out the results containing "call",

grep lcov * | grep -v call
...

Grep gives me every single line in my workspace that doesn't contain "call".

Environment Info:

This is happening in both bash and fish
I have aliased the grep command like so alias grep='grep -nR --color=always'

Anything else I might be missing?

Best Answer

The alias is what is causing it. From man grep, the -R option causes grep to "read all files under each directory, recursively". Hence, the part after the pipe ignores the output from the first grep, and instead greps through all files recursively from the current directory.

You can bypass the alias and use vanilla grep with \grep. Hence the following should give you what you expect.

grep lcov * | \grep -v call

However, I personally think that putting -R in the alias is confusing.

Related Solutions

Bash – Multicolored Grep

Here's a different approach. I have a little Perl script which I have already posted in another answer that will highlight the user provided patterns in different colors. A slightly modified version of the script will act like grep:

#!/usr/bin/env perl
use Getopt::Std;
use strict;
use Term::ANSIColor; 

my %opts;
getopts('hic:l:',\%opts);
    if ($opts{h}){
      print<<EoF; 
Use -l to specify the pattern(s) to highlight. To specify more than one 
pattern use commas. 

-l : A Perl regular expression to be colored. Multiple expressions can be
     passed as comma separated values: -l foo,bar,baz
-i : makes the search case sensitive
-c : comma separated list of colors;

EoF
      exit(0);
    }

my $case_sensitive=$opts{i}||undef;
my @color=('bold red','bold blue', 'bold yellow', 'bold green', 
       'bold magenta', 'bold cyan', 'yellow on_blue', 
       'bright_white on_yellow', 'bright_yellow on_red', 'white on_black');
if ($opts{c}) {
   @color=split(/,/,$opts{c});
}
my @patterns;
if($opts{l}){
     @patterns=split(/,/,$opts{l});
}
else{
    $patterns[0]='\*';
}

# Setting $| to non-zero forces a flush right away and after 
# every write or print on the currently selected output channel. 
$|=1;

while (my $line=<>) 
{ 
    my $want=0;
    for (my $c=0; $c<=$#patterns; $c++){
    if($case_sensitive){
        if($line=~/$patterns[$c]/){
           $line=~s/($patterns[$c])/color("$color[$c]").$1.color("reset")/ge;
           $want++;
        }
    }
    else{
        if($line=~/$patterns[$c]/i){
          $line=~s/($patterns[$c])/color("$color[$c]").$1.color("reset")/ige;
          $want++;
        }
      }
    }
print STDOUT $line if $want>0;
}

If you save that script as cgrep somewhere in your PATH and make it executable, you can specify up to 10 different patterns, each of which will be printed in a different color:

enter image description here

$ cgrep -h
Use -l to specify the pattern(s) to highlight. To specify more than one 
pattern use commas. 

-l : A Perl regular expression to be colored. Multiple expressions can be
     passed as comma separated values: -l foo,bar,baz
-i : makes the search case sensitive
-c : comma separated list of colors;

Grep Command – Troubleshooting Grep Errors

Since your gene names are always in the 2nd column of the file, you can use awk for this:

awk '
    {   ## while reading the first file, save name in the array a
        if(NR==FNR){a[$1]++;} 

        ## If this is the 2nd file
        else{
            ## print if the value of the second column is defined in the array 
            if($2 in a){print}
        }
    }' file1 file2

The same, condensed:

awk '{if(NR==FNR){a[$1]++;}else{if($2 in a){print}}}' file1 file2

more condensed:

awk '(NR==FNR){a[$1]++}($2 in a){print}' file1 file2

and truly minimalist (in answer to @Awk):

awk 'NR==FNR{a[$1]}$2 in a' file1 file2

Best Answer

Related Solutions

Bash – Multicolored Grep

Grep Command – Troubleshooting Grep Errors

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