Package dimer

source code

root package

Submodules

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dimer.archive: utilities and wrappers for working with HDF archives.
dimer.archive_tests
dimer.config: module that provides configuration file functionality
dimer.data: support for dataset IO and manipulation
dimer.data_tests
dimer.experiment: Created on Jul 11, 2013
dimer.filelock
dimer.genome: modules for dealing with (mainly importing to datasets) genomic data
- dimer.genome.bed: Iterator for the BED format ( http://genome.ucsc.edu/FAQ/FAQformat.html#format1 ) Returns chrom, chromStart, chromEnd, name, score
- dimer.genome.bedops: wrapper to some of the bedops (http://code.google.com/p/bedops/) utilities
- dimer.genome.bedops_tests
- dimer.genome.peak: Iterator for the broadPeak and narrowPeak formats (http://genome.ucsc.edu/FAQ/FAQformat.html#format13 and https://genome.ucsc.edu/FAQ/FAQformat.html#format12)
dimer.nnet: abstract classes for deep models
- dimer.nnet.autoencoder: autoencoders
- dimer.nnet.autoencoder_tests
- dimer.nnet.base_test_classes: abstract tester methods and common test operations
- dimer.nnet.config_spec: classes to handle configuration files
- dimer.nnet.cspec_tests
- dimer.nnet.monitor
- dimer.nnet.monitor_tests
- dimer.nnet.nccn: convolutional neural nets
- dimer.nnet.nccn_tests
- dimer.nnet.nnet_tests
- dimer.nnet.utils: This file contains different utility functions that are not connected in anyway to the networks presented in the tutorials, but rather help in processing the outputs into a more understandable way.
dimer.ops: common operations on numpy arrays

Functions

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measure_time(funct)
decorator that measures the time spent in a function

source code

deprecated(func)
This is a decorator which can be used to mark functions as deprecated.

source code

Variables

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log = logging.getLogger(__name__)

__package__ = 'dimer'

Function Details

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deprecated(func)

source code

This is a decorator which can be used to mark functions as deprecated. It will result in a warning being emmitted when the function is used.