Skip to content
Permalink
Browse files

Initial commit

  • Loading branch information
philres committed Nov 12, 2018
1 parent 95b4860 commit 5cffd35851ecb36e3504d798fad16bc1347fff2d
Showing with 16,185 additions and 0 deletions.
  1. +27 −0 .coveragerc
  2. +5 −0 .gitignore
  3. +2 −0 COPYRIGHT
  4. +33 −0 Dockerfile
  5. +363 −0 LICENSE.md
  6. +213 −0 README.md
  7. +5 −0 pytest.ini
  8. +6 −0 qcat/__init__.py
  9. +132 −0 qcat/adapters.py
  10. +47 −0 qcat/calibration.py
  11. +592 −0 qcat/cli.py
  12. +287 −0 qcat/config.py
  13. +183 −0 qcat/eval.py
  14. +241 −0 qcat/eval_full.py
  15. +105 −0 qcat/eval_roc.py
  16. +247 −0 qcat/layout.py
  17. +439 −0 qcat/resources/kits/DUAL_3p.yml
  18. +439 −0 qcat/resources/kits/DUAL_5p.yml
  19. +56 −0 qcat/resources/kits/LWB001_3p.yml
  20. +56 −0 qcat/resources/kits/LWB001_5p.yml
  21. +110 −0 qcat/resources/kits/NBD104_3p.yml
  22. +106 −0 qcat/resources/kits/NBD104_5p.yml
  23. +106 −0 qcat/resources/kits/NBD104_NBD114_3p.yml
  24. +105 −0 qcat/resources/kits/NBD104_NBD114_5p.yml
  25. +58 −0 qcat/resources/kits/NBD114_3p.yml
  26. +57 −0 qcat/resources/kits/NBD114_5p.yml
  27. +58 −0 qcat/resources/kits/PBC001_3p.yml
  28. +58 −0 qcat/resources/kits/PBC001_5p.yml
  29. +397 −0 qcat/resources/kits/PBC096_3p.yml
  30. +397 −0 qcat/resources/kits/PBC096_5p.yml
  31. +103 −0 qcat/resources/kits/RAB201_3p.yml
  32. +103 −0 qcat/resources/kits/RAB201_5p_a.yml
  33. +103 −0 qcat/resources/kits/RAB201_5p_c.yml
  34. +58 −0 qcat/resources/kits/RBK001.yml
  35. +55 −0 qcat/resources/kits/RBK004.yml
  36. +61 −0 qcat/resources/kits/RPB004_RLB001.yml
  37. +23 −0 qcat/resources/kits/VMK001.yml
  38. +483 −0 qcat/resources/kits/simple_extended.yml
  39. +99 −0 qcat/resources/kits/simple_standard.yml
  40. +124 −0 qcat/scanner.py
  41. +733 −0 qcat/scanner_base.py
  42. +140 −0 qcat/scanner_brill.py
  43. +146 −0 qcat/scanner_dual.py
  44. +141 −0 qcat/scanner_epi2me.py
  45. +126 −0 qcat/scanner_guppy.py
  46. +89 −0 qcat/scanner_simple.py
  47. 0 qcat/test/__init__.py
  48. +3,956 −0 qcat/test/data/barcode_1k.fastq
  49. +3,956 −0 qcat/test/data/nobarcode_1k.fastq
  50. +661 −0 qcat/test/test_barcode.py
  51. +42 −0 qcat/utils.py
  52. +7 −0 setup.cfg
  53. +46 −0 setup.py
  54. 0 test.ini
@@ -0,0 +1,27 @@
# .coveragerc to control coverage.py
[run]
branch = True
;include = /file/path/to/files
omit = */test/*,qcat/__init__.py,qcat/cli.py,qcat/eval.py,qcat/eval_full.py,qcat/eval_roc.py,qcat/scanner_brill.py

[report]
# Regexes for lines to exclude from consideration
exclude_lines =
# Have to re-enable the standard pragma
pragma: no cover

# Don't complain about missing debug-only code:
; def __repr__
; if self\.debug

# Don't complain if tests don't hit defensive assertion code:
raise AssertionError
raise NotImplementedError

# Don't complain if non-runnable code isn't run:
if 0:
if __name__ == .__main__.:
if __name__ == __main__:

ignore_errors = True

@@ -1 +1,6 @@
tmp/
.DS_Store
.idea/
*egg*
.pytest_cache
.coverage
@@ -0,0 +1,2 @@

(c) 2018 Oxford Nanopore Technologies Ltd.
@@ -0,0 +1,33 @@
FROM ubuntu:16.04
MAINTAINER prescheneder

COPY . /qcat/

RUN apt-get update \
&& apt-get install --no-install-recommends -y \
python3 \
python3-pip \
python3-dev \
build-essential \
time \
python3-pkg-resources \
autotools-dev \
autoconf \
libboost-all-dev \
&& pip3 --no-cache-dir install --upgrade \
setuptools \
wheel \
&& cd /qcat \
&& pip3 --no-cache-dir install . \
&& cd - \
&& rm -rf /qcat \
&& qcat -h \
# Cleanup \
&& apt-get remove --purge -y \
build-essential \
python3-dev \
autotools-dev \
autoconf \
&& apt autoremove --purge -y \
&& rm -rf /var/lib/apt/lists/*

0 comments on commit 5cffd35

Please sign in to comment.
You can’t perform that action at this time.