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grep not working ????

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# 1  
Old 01-04-2011
grep not working ????
Hi,

I've prob in doing grep. I want to grep line staring with number 531250 in the 1st column from a file (example in picture attached below)
grep not working ????-greppng

using command
Code:
grep -w "531250" file

my ideal result should be
Code:
531250  1       21      42.1    100     1e-05   rubber_UT_velvet.seq.Contig4570

instead it gives this output

Code:
21079   1       21      42.1    100     1e-05   NODE_50158_length_96_cov_5.531250
21079   1       21      42.1    100     1e-05   NODE_50158_length_96_cov_5.531250
23133   1       21      42.1    100     1e-05   NODE_50158_length_96_cov_5.531250
436591  1       21      42.1    100     1e-05   NODE_6486_length_160_cov_25.531250
531250  1       21      42.1    100     1e-05   rubber_UT_velvet.seq.Contig4570
594834  1       21      42.1    100     1e-05   NODE_50158_length_96_cov_5.531250
190670  1       21      42.1    100     1e-05   NODE_22903_length_224_cov_3.531250
287934  1       21      42.1    100     1e-05   NODE_58392_length_96_cov_2.531250

From the false result, I can see the grep find line that also contain 531250 but not exact one. I've already invoke grep -w option but still showing the same prob. Smilie

Hope somebody can help me with this.

Thanks in advance
Last edited by masterpiece; 01-09-2011 at 11:50 PM..
# 2  
Old 01-04-2011
Code:
grep '^531250' file

This User Gave Thanks to Franklin52 For This Post:
masterpiece
# 3  
Old 01-04-2011
From grep:
Anchoring
The caret ^ and the dollar sign $ are meta-characters that respectively match the empty string at the beginning and end of a line.
So you need to use:
Code:
grep -w ^531250 file

Last edited by m.d.ludwig; 01-04-2011 at 07:48 AM.. Reason: typo
This User Gave Thanks to m.d.ludwig For This Post:
masterpiece
# 4  
Old 01-04-2011
Quote:
Originally Posted by masterpiece
Hi,

I've prob in doing grep. I want to grep line staring with number 531250 in the 1st column from a file (example in picture attached below)
Attachment 1745

using command grep -w "531250" file

my ideal result should be

531250 1 21 42.1 100 1e-05 rubber_UT_velvet.seq.Contig4570

instead it gives this output

21079 1 21 42.1 100 1e-05 NODE_50158_length_96_cov_5.531250
21079 1 21 42.1 100 1e-05 NODE_50158_length_96_cov_5.531250
23133 1 21 42.1 100 1e-05 NODE_50158_length_96_cov_5.531250
436591 1 21 42.1 100 1e-05 NODE_6486_length_160_cov_25.531250
531250 1 21 42.1 100 1e-05 rubber_UT_velvet.seq.Contig4570
594834 1 21 42.1 100 1e-05 NODE_50158_length_96_cov_5.531250
190670 1 21 42.1 100 1e-05 NODE_22903_length_224_cov_3.531250
287934 1 21 42.1 100 1e-05 NODE_58392_length_96_cov_2.531250

From the false result, I can see the grep find line that also contain 531250 but not exact one. I've already invoke grep -w option but still showing the same prob. Smilie

Hope somebody can help me with this.

Thanks in advance
Code:
grep '^531250' inputfile

gives the expected output.

regards
# 5  
Old 01-04-2011
Not to be a pita, but:
Code:
grep '^531250' inputfile

is not correct, for while it will match:
Code:
531250  1       21      42.1    100     1e-05   rubber_UT_velvet.seq.Contig4570

it will also match:
Code:
531250187423987423987324987432

which was not intended, as per:
Quote:
Originally Posted by masterpiece
<snip>
I want to grep line staring with number 531250 in the 1st column from a file
<snip>
The -w option is needed, or the regex needs to be ^531250[[:space:]], although that would not select any line containing only the specified number.
# 6  
Old 01-04-2011
Quote:
Originally Posted by m.d.ludwig
Not to be a pita, but:
Code:
grep '^531250' inputfile

is not correct, for while it will match:
Code:
531250  1       21      42.1    100     1e-05   rubber_UT_velvet.seq.Contig4570

it will also match:
Code:
531250187423987423987324987432

which was not intended
The given solution is based on the given input file, I don't see any line like that.
# 7  
Old 01-04-2011
Hi all,

Thanks for the solutions. Really helpful.

After I banged my head to wall several times I've come out with another solution by using awk

Code:
awk '{if ($1==531250) print}' file

will also give the output that i want.


But from my understanding about grep, option '-w' will only grep exact string right? In other word, apart from my ideal output the rest should have not apear right? Or am i missing something Smilie
Last edited by masterpiece; 01-09-2011 at 11:51 PM..
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