Commit 915099fd authored by Andreas Tille's avatar Andreas Tille

Imported Upstream version 0.0.20130418

parents
Help on python script fitGCP.py
Fits mixtures of probability distributions to genome coverage profiles using an
EM-like iterative algorithm.
The script uses a SAM file as input and parses the mapping information and
creates a Genome Coverage Profile (GCP). The GCP is written to a file, such that
this step can be skipped the next time.
The user provides a mixture model that is fitted to the GCP. Furthermore, the
user may specify initial parameters for each model.
As output, the script generates a text file containing the final set of fit
parameters and additional information about the fitting process. A log file
contains the the current set of parameters in each step of the iteration. If
requested, a plot of the GCP and the fitted distributions can be created.
REQUIREMENTS:
-------------------------------------------------------------------------------
Python 2.7
Python packages numpy, scipy, pysam
USAGE:
-------------------------------------------------------------------------------
fitGCP runs on the command line. The following command describes the general
structure:
python fitGCP.py [options] NAME
fitGCP fits mixtures of probability distributions to genome coverage profiles using
an EM-like iterative algorithm.
The script uses a SAM file as input and parses the mapping information and
creates a Genome Coverage Profile (GCP). The GCP is written to a file, such that
this step can be skipped the next time.
The user provides a mixture model that is fitted to the GCP. Furthermore, the
user may specify initial parameters for each model.
As output, the script generates a text file containing the final set of fit
parameters and additional information about the fitting process. A log file
contains the the current set of parameters in each step of the iteration. If
requested, a plot of the GCP and the fitted distributions can be created.
Parameters:
NAME: Name of SAM file to analyze.
Options:
-h, --help show this help message and exit
-d DIST, --distributions=DIST
Distributions to fit. z->zero; n: nbinom (MOM); N:
nbinom (MLE); p:binom; t: tail. Default: zn
-i STEPS, --iterations=STEPS
Maximum number of iterations. Default: 50
-t THR, --threshold=THR
Set the convergence threshold for the iteration. Stop
if the change between two iterations is less than THR.
Default: 0.01
-c CUTOFF, --cutoff=CUTOFF
Specifies a coverage cutoff quantile such that only
coverage values below this quantile are considered.
Default: 0.95
-p, --plot Create a plot of the fitted mixture model. Default:
False
-m MEAN, --means=MEAN
Specifies the initial values for the mean of each
Poisson or Negative Binomial distribution. Usage: -m
12.4 -m 16.1 will specify the means for the first two
non-zero/tail distributions. The default is calculated
from the data.
-a ALPHA, --alpha=ALPHA
Specifies the initial values for the proportion alpha
of each distribution. Usage: For three distributions
-a 0.3 -a 0.3 specifies the proportions 0.3, 0.3 and
0.4. The default is equal proportions for all
distributions.
-l, --log Enable logging. Default: False
--view Only view the GCP. Do not fit any distribution.
Respects cutoff (-c). Default: False
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