txt2odf (v2)

This module will turn a TXT file into ComparativeMarkerSelectionViewer-compatible ODF file.

Author: Edwin Juarez

Contact:

https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!forum/genepattern-help

Module creator: ejuarez@ucsd.edu

Algorithm Version:

Summary

This module will turn a TXT file into ComparativeMarkerSelectionViewer-compatible ODF file.

 

Technical notes:

 

  • This module has been tested to run in the Docker container genepattern/docker-python36:release-0.2 which has build code bj4fefqe2da2fnopdywxz3x
  • To create a conda environment (called GP_hierarchical_clustering_env) with the required dependencies download the requirements.txt file from the github repository named genepattern/docker-python36 (here is the url of the file: https://raw.githubusercontent.com/genepattern/docker-python36/master/requirements.txt) and run this three commands in the same folder where requirements.txt is located:

conda create --name GP_txt2odf_env pip
source activate GP_txt2odf_env
pip install -r requirements.tx

Parameters

Name Description
txt file * The text file to be reformatted
prune gct *

Whether or not to prune the GCT file to match the TXT file. If you are using the text file created by DESeq2, set this parameter to True.
gct

This is the GCT file which was originally used (e.g., the input to DESeq2). Set prune_gct to True if you want this file pruned.
cls This is the CLS file which was originally used (e.g., the input to DESeq2).

* - required

Output Files

  1. ODF file
    Contains the original data, but reformatted to be compatible with ComparativeMarkerSelectionViewer.
  2. Pruned GCT file
    This is a GCT file which contains the same rows as the text file provided.

License

txt2odf is distributed under a modified BSD license available at https://raw.githubusercontent.com/genepattern/txt2odf/master/LICENSE

Platform Dependencies

Task Type:
File format

CPU Type:
any

Operating System:
any

Language:
Python 3.6

Version Comments

Version Release Date Description
2 2018-03-30 Small text modifications
1 2018-03-21 First version