Darts_DNN package

Subpackages

• Darts_DNN.resources package
  • Module contents

Submodules

Darts_DNN.Darts_build_feature module

Darts_DNN.Darts_get_data module

Darts_DNN - get_data

Implements an internal downloading module for getting data from internet. Data includes training data, cis feature files, etc.

This module depends on the url and md5sum stored in resources/download.yaml

Darts_DNN.Darts_get_data.parser(args)

Darts_DNN.Darts_pred module

Darts_DNN.Darts_rbpTable module

Darts_DNN - rbpTable

Utilities for reading and preparinig trans features from gene expression

Darts_DNN.Darts_rbpTable.make_rbp_exp_table(target, control, darts_dir, RBP, RBP_geneName, s1, s2)

Darts_DNN.Darts_rbpTable.parser(outdir, kallisto_1, kallisto_2)

Darts_DNN.Darts_rbpTable.read_kal_fn(tsv_fn_list)

Darts_DNN.Darts_rbpTable.read_rbp_list(rbp_str)

Darts_DNN.Darts_rbpTable.upper_quantile_normalization(gene_exp)

Darts_DNN.Darts_train module

Darts_DNN.Darts_tx2g module

Darts_DNN - tx2g

Mapping kallisto transcript TPM to Gene

Todo

parse a GTF file for mapping IDs in the future

Darts_DNN.Darts_tx2g.kallisto2rsem(kal_dir, t2g)

Darts_DNN.Darts_tx2g.parser(kal_dir)

Darts_DNN.Darts_tx2g.read_kallisto(fn, t2g)

Darts_DNN.Darts_tx2g.read_t2g()

Darts_DNN.Darts_tx2g.write_out_comparison(rsem_dict, kal_dict, fn)

Darts_DNN.Darts_tx2g.write_out_quant(kal_dict, fn)

Darts_DNN.config module

Here are general configurations for the Darts_DNN package, including version control, trained model parameter, etc.

Darts_DNN.config.substitute_home_directory(d)

Darts_DNN.download module

Python Code for downloading and checking md5sum from https://gist.github.com/mjohnsullivan/9322154

Darts_DNN.download.download_with_resume(url, file_path, hash=None, timeout=10)

Performs a HTTP(S) download that can be restarted if prematurely terminated. The HTTP server must support byte ranges. :param file_path: the path to the file to write to disk :type file_path: string :param hash: hash value for file validation :type hash: string (MD5 hash value)

Darts_DNN.download.validate_file(file_path, hash)

Validates a file against an MD5 hash value :param file_path: path to the file for hash validation :type file_path: string :param hash: expected hash value of the file :type hash: string – MD5 hash value

Darts_DNN.sklearn_nn module

Darts_DNN.utils module

Module contents