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Removing low frequency sequences

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# 1  
Old 06-24-2010
Removing low frequency sequences
If I have a file with the following information
Quote:
>GHL8OVD01BNNCA Freq 2
TTGATGTGCCCGTGGGTTTCCCGTCAACACCGGCAAATAGTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01CMQVT Freq 15
TTGATGTCGTGGGTTTCCCGTCAACACCGGCAAATAGTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01BNNCF Freq 2
TTGATGTGCCAGCTGCACTTCCCCCGGTGACGTGGGTTTCCCGTCTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01CMQVW Freq 11
TTGATGTGTCCCGTCGACACCGGCAAATAGCAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01A45V3 Freq 9
TTGATTCCCGTCGACACCGGCAAATAGCAGCAGCACTACAGGACCTTCGCCCA
>GHL8OVD01B9PRR Freq 1
TTGATGTGCCAGCTTTCGCGTCGACACCGGCAAATAGTAGCAGCGCTACCAGGACCTTCGCCCA
>GHL8OVD01BL8BD Freq 4
TTGATGAGTACTTCCCCCGGTGACGTGGGTCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01AV2U9 Freq 17
TTGATGTGCCAACTAGCAAGACTGCGCGTGCAAATAGTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01BJX6A Freq 3
TTGATGTGCCAGCTGCCGTTGTCCCCCGGTGACGTGGGTCTCCCGTCGAGGACCTTCGCCCA
>GHL8OVD01A9D5T Freq 1
TGATGTGCCAGCCCCGGTGACGTGGGTTTCCGGTCGACATTCGCCCA
And I would like to remove all the sequences with Freq less than 3, so I end up having the following file:
Quote:
>GHL8OVD01CMQVT Freq 15
TTGATGTCGTGGGTTTCCCGTCAACACCGGCAAATAGTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01CMQVW Freq 11
TTGATGTGTCCCGTCGACACCGGCAAATAGCAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01A45V3 Freq 9
TTGATTCCCGTCGACACCGGCAAATAGCAGCAGCACTACAGGACCTTCGCCCA
>GHL8OVD01BL8BD Freq 4
TTGATGAGTACTTCCCCCGGTGACGTGGGTCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01AV2U9 Freq 17
TTGATGTGCCAACTAGCAAGACTGCGCGTGCAAATAGTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01BJX6A Freq 3
TTGATGTGCCAGCTGCCGTTGTCCCCCGGTGACGTGGGTCTCCCGTCGAGGACCTTCGCCCA
I am currently using awk to accomplish this task but I am not getting the results I actually want.
Any help will be greatly appreciated.
Last edited by Xterra; 06-24-2010 at 04:31 PM..
# 2  
Old 06-24-2010
Code:
awk '/^>/{if ($3<=2){getline;next}}1' file

# 3  
Old 06-24-2010
Hi.

I think you mean less than 3? (based on your output)

Code:
$ awk '$2 == "Freq" { ($3<3)?P=0:P=1}P' file1
>GHL8OVD01CMQVT Freq 15
TTGATGTCGTGGGTTTCCCGTCAACACCGGCAAATAGTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01CMQVW Freq 11
TTGATGTGTCCCGTCGACACCGGCAAATAGCAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01A45V3 Freq 9
TTGATTCCCGTCGACACCGGCAAATAGCAGCAGCACTACAGGACCTTCGCCCA
>GHL8OVD01BL8BD Freq 4
TTGATGAGTACTTCCCCCGGTGACGTGGGTCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01AV2U9 Freq 17
TTGATGTGCCAACTAGCAAGACTGCGCGTGCAAATAGTAGCAGCACTACCAGGACCTTCGCCCA
>GHL8OVD01BJX6A Freq 3
TTGATGTGCCAGCTGCCGTTGTCCCCCGGTGACGTGGGTCTCCCGTCGAGGACCTTCGCCCA

This User Gave Thanks to Scott For This Post:
guruprasadpr
# 4  
Old 06-24-2010
Your example uses less than or equal to two.... which is what this does:
Code:
 awk ' /^>/ && $NF>2 {ok=1}
       /^>/ && $NF<3 {ok=0}
       ok {print $0} ' filename

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