I have a CSV file that looks like
0,0,0,0,1,0,1,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,2,0,0,0,0,0,0
10,11,7,0,4,12,2,3,7,0,11,3,12,4,0,5,5,4,5,0,8,6,12,0,9,3,3,0,2,7,8
19,11,7,0,4,14,16,10,8,2,13,7,15,6,0,76,6,4,10,0,18,10,17,1,11,3,3,0,9,9,8... (7 Replies)
Hi all,
I am new to shell scripting and wanna calculate the mean and standard deviation using shell programming.
I have a file with letters that are repeating and their corresponding duration
a 0.32
a 0.89
aa 0.34
aa 0.23
au 0.012
au 0.26... (4 Replies)
Hi all,
I want to calculate the standard deviation for a column (happens to be column 3).
Does any know of simple awk script to do this?
Thanks (1 Reply)
Hi I want to use awk to print avg and st deviation but it does not go into a file for column 1 only.
I can do average and # of records but i cannot get st deviation.
awk '{sum+=$1} END { print "Average = ",sum/NR}'
thanks (1 Reply)
Hello,
I'm trying to create a shell script (#!/bin/sh) which should tell me the age of a file in minutes...
I have a process, which delivers me all 15 minutes a new file and I want to have a monitoring script, which sends me an email, if the present file is older than 20 minutes.
To do... (10 Replies)
Hi all,
I need to find the standard deviation of each column of a dataset below for each hour. The data is given in 5 second intervals as shown below
DATE TIME FRAC_DAYS_SINCE_JAN1 FRAC_HRS_SINCE_JAN1 EPOCH_TIME ... (11 Replies)
I have a file with say 50 columns, each containing a whole lot of data.
Each column contains data from a separate simulation, but each simulation is related to the data in the last (REFERENCE) column $50
I need to calculate the RMS deviation for each data line, i.e. column 1 relative to... (12 Replies)
Hi All,
I want someone to modify the below script from this forum so that it can be used for all columns in the file( instead of only printing column 3 mean and standard deviation values). I don't know how to loop around all the columns.
... (3 Replies)
I have a file that looks that this:
820 890 530
1650 1600 1800
1850 1900 2270
1640 2300 1670
2080 2200 2350
1150 1630 2210
I would like to output the mean and standard deviation of each row so that my final output would look like this
820 890 530 746.667 155.849
1650 1600 1800... (5 Replies)
Dear all,
I need a little help. I am working on a frequency driven database in which the structure is as under:
headword=gloss<space>Frequency
The data which I am working with has dupes i.e. the Headword is repeated more than once with a different gloss variant on the right hand side and... (8 Replies)
Discussion started by: gimley
8 Replies
LEARN ABOUT DEBIAN
tigr-build-icm
TIGR-GLIMMER (1) (1) General Commands Manual TIGR-GLIMMER (1) (1)
NAME
tigr-glimmer -- Ceates and outputs an interpolated Markov model(IMM)
SYNOPSIS
tigr-build-icm
DESCRIPTION
Program build-icm.c creates and outputs an interpolated Markov model (IMM) as described in the paper A.L. Delcher, D. Harmon, S. Kasif,
O. White, and S.L. Salzberg. Improved Microbial Gene Identification with Glimmer. Nucleic Acids Research, 1999, in press. Please refer-
ence this paper if you use the system as part of any published research.
Input comes from the file named on the command-line. Format should be one string per line. Each line has an ID string followed by white
space followed by the sequence itself. The script run-glimmer3 generates an input file in the correct format using the 'extract' program.
The IMM is constructed as follows: For a given context, say acgtta, we want to estimate the probability distribution of the next character.
We shall do this as a linear combination of the observed probability distributions for this context and all of its suffixes, i.e., cgtta,
gtta, tta, ta, a and empty. By observed distributions I mean the counts of the number of occurrences of these strings in the training set.
The linear combination is determined by a set of probabilities, lambda, one for each context string. For context acgtta the linear combi-
nation coefficients are:
lambda (acgtta) (1 - lambda (acgtta)) x lambda (cgtta) (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x lambda (gtta) (1 - lambda (acgtta)) x
(1 - lambda (cgtta)) x (1 - lambda (gtta)) x lambda (tta) (1 - lambda (acgtta)) x (1 - lambda (cgtta)) x (1 - lambda (gtta)) x (1 - lambda
(tta)) x (1 - lambda (ta)) x (1 - lambda (a))
We compute the lambda values for each context as follows: - If the number of observations in the training set is >= the constant SAM-
PLE_SIZE_BOUND, the lambda for that context is 1.0 - Otherwise, do a chi-square test on the observations for this context compared to the
distribution predicted for the one-character shorter suffix context. If the chi-square significance < 0.5, set the lambda for this context
to 0.0 Otherwise set the lambda for this context to: (chi-square significance) x (# observations) / SAMPLE_WEIGHT
To run the program:
build-icm <train.seq > train.model
This will use the training data in train.seq to produce the file train.model, containing your IMM.
SEE ALSO
tigr-glimmer3 (1), tigr-long-orfs (1), tigr-adjust (1), tigr-anomaly (1), tigr-extract (1), tigr-check (1), tigr-codon-usage (1), tigr-
compare-lists (1), tigr-extract (1), tigr-generate (1), tigr-get-len (1), tigr-get-putative (1),
http://www.tigr.org/software/glimmer/
Please see the readme in /usr/share/doc/tigr-glimmer for a description on how to use Glimmer3.
AUTHOR
This manual page was quickly copied from the glimmer web site and readme file by Steffen Moeller moeller@debian.org for the Debian system.
TIGR-GLIMMER (1) (1)