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:
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Python 2.7
Python packages numpy, scipy, pysam
USAGE:
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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
