.gitignore

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

# surag
*DS_Store
*.bed
*.bed.gz
*.tagAlign.gz
*.tagAlign
*.narrowPeak.gz
*.cts
*.fa
*.fai
*.npz
*.npy
*.pth
*.bw
*.bam
*.bai
*.bigwig
*.mat.gz
homer/
gimmemotifs/
*tmp*
lsgkm/
gene_lists/
gene_sets/
.*
*.log
*.pickle
BINDetect/ 
resources/
!.gitignore
*.intersect.txt
*.mm
*.hdf5
*.h5
*.pfm
*.meme
*.homer
*.hits
*.scan
features*.tsv
*seurat.rds
*.h5ad
image.png
*density.txt
*.motif 
*.quant
*.bg
image.png
image.jpg

# surag -- analysis specific
src/analysis/20200416_cicero/out/
src/analysis/20200216_heterokaryon_similarity/data/20200518_n76052/*counts*.tsv
src/analysis/20200216_heterokaryon_similarity/data/20200518_n76052/*peaks*.tsv
src/analysis/20200711_naive_vs_primed/data/*counts*.tsv
src/analysis/20200723_motif_annotation/bpnet_scores/20200705_gridmap_peakwidthnorm_logplusznorm_4way_ordered_n40/block_ism
src/analysis/20200723_motif_annotation/bpnet_scores/20201020_n62402/block_ism
src/analysis/20200925_Peak2Gene/peak2gene_links
*contrib_*.png
src/analysis/20210310_autogenerate_loci_plots/plots/
src/analysis/20200828_RNA_Seurat/sessions/20210725_n59378/atac.20210717_n62599.harmony.cca.feat.tsv

# surag -- abandoned analyses/archived/do not track
src/analysis/20200117_EDA/
src/analysis/20200122_snapATAC/snapATAC_sessions/20200125_n76770
src/analysis/20200131_ENCODE_match/data/
src/analysis/20200206_pmat_snapATAC/sessions/20200217_n71173/
src/analysis/20200206_pmat_snapATAC/sessions/20200220_n74838/
src/analysis/20200206_pmat_snapATAC/out/
src/analysis/20200206_pmat_snapATAC/sessions/20200520_n68916/fine_clusters.tsv
src/analysis/20200212_poincare/FeatureMatrix/
src/analysis/20200217_trajectory/figures/
src/analysis/20200217_trajectory/sessions/20200223_n74838/
src/analysis/20200329_ref_similarity
src/analysis/20200607_ChromVAR/out/20200520_n68916
src/analysis/20200706_iPSC_CTCF_vs_CTCFL

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
pip-wheel-metadata/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# 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/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# PyBuilder
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# pyenv
.python-version

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

# PEP 582; used by e.g. github.com/David-OConnor/pyflow
__pypackages__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/