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..
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LEARN ABOUT OPENSOLARIS
mlib_signalmelcepstral_f32
mlib_SignalMelCepstral_F32(3MLIB) mediaLib Library Functions mlib_SignalMelCepstral_F32(3MLIB)
NAME
mlib_SignalMelCepstral_F32 - perform cepstral analysis in mel frequency scale
SYNOPSIS
cc [ flag... ] file... -lmlib [ library... ]
#include <mlib.h>
mlib_status mlib_SignalMelCepstral_F32(mlib_f32 *cepst,
const mlib_f32 *signal, void *state);
DESCRIPTION
The mlib_SignalMelCepstral_F32() function performs cepstral analysis in mel frequency scale.
The first two steps of mel scale cepstral analysis is the same as in general cepstral anaysis. After the logarithm of the spectrum magni-
tude is obtained, it is converted into mel frequency scale before the inverse Fourier transform.
+-----------+ +-----------+
| Linear | | Inverse |
... ------>| to |------->| Fourier |----->
X'(k) | Mel Scale | X''(m) | Transform | c(n)
+-----------+ +-----------+
where X'(k) is defined in linear frequency scale and X''(m) is defined in mel frequency scale.
The mel frequency scale is defined as following.
freq_mel = melmul * LOG10(1 + freq_linear / meldiv)
where freq_mel is the frequency in mel scale, freq_linear is the frequency in linear scale, melmul is the multiplying factor, muldiv is the
dividing factor.
Optionally, a bank of band pass filters in linear frequency scale can be used below the bank of band pass filters in mel frequency scale,
as shown below in linear frequency scale.
0 f1 f2 f3 fp fp+1 fp+2 fp+3 fp+q
|---|---|---| ... |---|----|-----| ... | ... -> freq
where fp = melbgn, fp+q = melend, p = nlinear, q = nmel; the filters number 1 to p are defined in linear frequency scale which have equal
bandwidth in linear frequency scale; the filters number p+1 to p+q are defined in mel frequency scale which have equal bandwidth in mel
frequency scale and increasing bandwidth in linear frequency scale.
See Digital Signal Processing by Alan V. Oppenheim and Ronald W. Schafer, Prentice Hall, 1974.
See Fundamentals of Speech Recognition by Lawrence Rabiner and Biing-Hwang Juang, Prentice Hall, 1993.
PARAMETERS
The function takes the following arguments:
cepst The cepstral coefficients.
signal The input signal vector.
state Pointer to the internal state structure.
RETURN VALUES
The function returns MLIB_SUCCESS if successful. Otherwise it returns MLIB_FAILURE.
ATTRIBUTES
See attributes(5) for descriptions of the following attributes:
+-----------------------------+-----------------------------+
| ATTRIBUTE TYPE | ATTRIBUTE VALUE |
+-----------------------------+-----------------------------+
|Interface Stability |Committed |
+-----------------------------+-----------------------------+
|MT-Level |MT-Safe |
+-----------------------------+-----------------------------+
SEE ALSO
mlib_SignalMelCepstralInit_F32(3MLIB), mlib_SignalMelCepstralFree_F32(3MLIB), attributes(5)
SunOS 5.11 2 Mar 2007 mlib_SignalMelCepstral_F32(3MLIB)