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Deleting row if all column values are a particular string

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Top Forums Shell Programming and Scripting Deleting row if all column values are a particular string
# 8  
Old 10-19-2012
This is what I type:

mep74-1Smilieesktop morganmouchka$ awk '{n=0;for(i=2;i<=5;i++) if ($i+0!=0) n++}n' FS=',' AT_counts.txt

And nothing prints on the screen and it directs me to the next command line. (i.e. mep74-1Smilieesktop morganmouchka$
# 9  
Old 10-19-2012
Quote:
Originally Posted by vgersh99
Code:
awk '{n=0;for(i=2;i<=5;i++) if ($i+0!=0) n++}n' FS=',' myFile

This will also remove those lines whose 2nd,3rd,4th or 5th fields have either zeroes, white-space, null values or a string starting with a non-digit character (with or without white-space at the beginning).
Last edited by elixir_sinari; 10-19-2012 at 02:09 PM..
# 10  
Old 10-19-2012
Quote:
Originally Posted by mouchkam
This is what I type:

Code:
mep74-1:Desktop morganmouchka$ awk '{n=0;for(i=2;i<=5;i++) if ($i+0!=0) n++}n' FS=',' AT_counts.txt

And nothing prints on the screen and it directs me to the next command line. (i.e. mep74-1Smilieesktop morganmouchka$
Check your AT_counts.txt file - make sure it's formatted as your posted file. Any ^M characters?
I quoted the output of the script ran against your sample file above.
# 11  
Old 10-19-2012
Quote:
Originally Posted by vgersh99
Check your AT_counts.txt file - make sure it's formatted as your posted file. Any ^M characters?
I quoted the output of the script ran against your sample file above.
Okay...the data above was just made-up data to avoid the lengthy name of contigs. My data is in a tab delimited text file and looks as follows:

Code:
Locus_36635_Transcript_1/1_Confidence_1.000_Length_246    0    0    0    0
Locus_21231_Transcript_1/1_Confidence_1.000_Length_443    0    0    0    0
Locus_6145_Transcript_1/1_Confidence_1.000_Length_2892    0    0    0    0
Locus_16925_Transcript_1/1_Confidence_1.000_Length_838    0    0    0    0
Locus_125599_Transcript_2/4_Confidence_1.000_Length_409    0    2    0    4
Locus_90716_Transcript_1/1_Confidence_0.000_Length_1868    0    0    0    0

I'm obviously very new to Unix/Linux and I'm not sure I understand what ^M characters are or how to remove them? Should I used a different file format?
Moderator's Comments:
Mod Comment
Please use code tags when posting data and code samples!
Last edited by vgersh99; 10-19-2012 at 02:45 PM.. Reason: once again - please use code tags!
# 12  
Old 10-19-2012
Code:
 
awk '!($2==0 && $3==0 && $4==0 && $5==0)' infile

# 13  
Old 10-19-2012
Quote:
Originally Posted by rdrtx1
Code:
 
awk '!($2==0 && $3==0 && $4==0 && $5==0)' infile

When I run this code, it removes all rows with any zeros in columns 2-5 (e.g. 0 0 1 1 or
0 1 1 1 get removed), not just rows for which there are zeros in every column (e.g. 0 0 0 0 ).
# 14  
Old 10-19-2012
Quote:
Originally Posted by elixir_sinari
This will also remove those lines whose 2nd,3rd,4th or 5th fields have either zeroes, white-space, null values or a string starting with a non-digit character (with or without white-space at the beginning).
true, but your suggestion doesn't pick the all-zero condition (at least under Cygwin).
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