.gitignore

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]

# C extensions
*.so

# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
parts/
sdist/
*.egg-info/
.installed.cfg
*.egg

# PyInstaller
#  Usually these files are written by a python script from a template
#  before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.cache
nosetests.xml
coverage.xml

# Translations
*.mo
*.pot

# Django stuff:
*.log

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# vim
*.swo
*.swp

# textedit
*~

# openoffice
.~lock.*#

# a temporary folder
temp/

# binary data that is generally pickle files
Biochemistry/binary_data

# pycharm files
.idea/

# ipython notebook
.ipynb_checkpoints/

# for the cluster

sge/


# pickle files for the models
models/pickles/*.p

# cmake
CMakeCache.txt 
CMakeFiles
cmake_install.cmake
cmake-build-debug/*
CMakeCache.txt
install_manifest.txt

# compiled file
bin/fastq2fasta
bin/count_fasta
bin/fastq_avqual
bin/fastq_average_qual

# a virtual environment for anthill
venv_anthill/

# compiled version of the nw code
percent_pairwise_identity/needleman_wunsch-0.3.5/needleman_wunsch

# repeatfinder
*/core
testrepeatfinder/repeatFinder
repeatFinder

# virtual environment
venv/
venv_linux/

# some compiled code
bin/primer-basecounting
bin/primer-predictions
bin/primer-trimming
bin/count_fastq
bin/fastg2gfa
fastq/change_fastq_pair_symbol
fastq/filter_fastq_length
bangers
rob_tests/hashes
bin/fasta_split

jupyter/*.png