From 53ea1c71eaca48175b455b07e68cc3af1de5a0eb Mon Sep 17 00:00:00 2001
From: Jeremy Mathews <Jeremy.Mathews@utsouthwestern.edu>
Date: Tue, 16 Jul 2019 14:19:52 -0500
Subject: [PATCH] import shutils
---
README.md | 30 +++++++++----------
.../tests/test_pool_and_psuedoreplicate.py | 4 +--
2 files changed, 17 insertions(+), 17 deletions(-)
diff --git a/README.md b/README.md
index e236165..546d6ff 100644
--- a/README.md
+++ b/README.md
@@ -133,22 +133,22 @@ If you find an error, please let the [BICF](mailto:BICF@UTSouthwestern.edu) know
Please cite individual programs and versions used [HERE](docs/references.md), and the pipeline doi:[10.5281/zenodo.2648844](https://doi.org/10.5281/zenodo.2648844). Please cite in publications: Pipeline was developed by BICF from funding provided by Cancer Prevention and Research Institute of Texas (RP150596).
## Programs and Versions
- + python/3.6.1-2-anaconda [website](https://www.anaconda.com/download/#linux) [citation](docs/references.txt)
- + trimgalore/0.4.1 [website](https://github.com/FelixKrueger/TrimGalore) [citation](docs/references.txt)
- + cutadapt/1.9.1 [website](https://cutadapt.readthedocs.io/en/stable/index.html) [citation](docs/references.txt)
- + bwa/intel/0.7.12 [website](http://bio-bwa.sourceforge.net/) [citation](docs/references.txt)
- + samtools/1.6 [website](http://samtools.sourceforge.net/) [citation](docs/references.txt)
- + sambamba/0.6.6 [website](http://lomereiter.github.io/sambamba/) [citation](docs/references.txt)
- + bedtools/2.26.0 [website](https://bedtools.readthedocs.io/en/latest/) [citation](docs/references.txt)
- + deeptools/2.5.0.1 [website](https://deeptools.readthedocs.io/en/develop/) [citation](docs/references.txt)
- + phantompeakqualtools/1.2 [website](https://github.com/kundajelab/phantompeakqualtools) [citation](docs/references.txt)
- + macs/2.1.0-20151222 [website](http://liulab.dfci.harvard.edu/MACS/) [citation](docs/references.txt)
- + UCSC_userApps/v317 [website](https://genome.ucsc.edu/util.html) [citation](docs/references.txt)
- + R/3.4.1 [website](https://www.r-project.org/) [citation](docs/references.txt)
+ + python/3.6.1-2-anaconda [website](https://www.anaconda.com/download/#linux) [citation](docs/references.md)
+ + trimgalore/0.4.1 [website](https://github.com/FelixKrueger/TrimGalore) [citation](docs/references.md)
+ + cutadapt/1.9.1 [website](https://cutadapt.readthedocs.io/en/stable/index.html) [citation](docs/references.md)
+ + bwa/intel/0.7.12 [website](http://bio-bwa.sourceforge.net/) [citation](docs/references.md)
+ + samtools/1.6 [website](http://samtools.sourceforge.net/) [citation](docs/references.md)
+ + sambamba/0.6.6 [website](http://lomereiter.github.io/sambamba/) [citation](docs/references.md)
+ + bedtools/2.26.0 [website](https://bedtools.readthedocs.io/en/latest/) [citation](docs/references.md)
+ + deeptools/2.5.0.1 [website](https://deeptools.readthedocs.io/en/develop/) [citation](docs/references.md)
+ + phantompeakqualtools/1.2 [website](https://github.com/kundajelab/phantompeakqualtools) [citation](docs/references.md)
+ + macs/2.1.0-20151222 [website](http://liulab.dfci.harvard.edu/MACS/) [citation](docs/references.md)
+ + UCSC_userApps/v317 [website](https://genome.ucsc.edu/util.html) [citation](docs/references.md)
+ + R/3.4.1 [website](https://www.r-project.org/) [citation](docs/references.md)
+ SPP/1.14
- + meme/4.11.1-gcc-openmpi [website](http://meme-suite.org/doc/install.html?man_type=web) [citation](docs/references.txt)
- + ChIPseeker [website](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) [citation](docs/references.txt)
- + DiffBind [website](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) [citation](docs/references.txt)
+ + meme/4.11.1-gcc-openmpi [website](http://meme-suite.org/doc/install.html?man_type=web) [citation](docs/references.md)
+ + ChIPseeker [website](https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html) [citation](docs/references.md)
+ + DiffBind [website](https://bioconductor.org/packages/release/bioc/html/DiffBind.html) [citation](docs/references.md)
diff --git a/workflow/tests/test_pool_and_psuedoreplicate.py b/workflow/tests/test_pool_and_psuedoreplicate.py
index ef8d268..edc1f24 100644
--- a/workflow/tests/test_pool_and_psuedoreplicate.py
+++ b/workflow/tests/test_pool_and_psuedoreplicate.py
@@ -5,6 +5,7 @@ import pandas as pd
from io import StringIO
import os
import pool_and_psuedoreplicate
+import shutil
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/design/'
@@ -63,8 +64,7 @@ def test_check_controls_single(design_experiment_3):
@pytest.mark.unit
def test_single_rep(design_experiment_2):
cwd = os.getcwd()
- B_1 = open(cwd + '/B_1.bedse.gz', "w+")
- B_1.close()
+ shutil.copy('/work/BICF/s189701/chipseq_analysis/test_data/B_1.bedse.gz', cwd)
single_rep = pool_and_psuedoreplicate.generate_design('false', 1.2, design_experiment_2, cwd, 1, 1)
--
GitLab