toulligqc 2.5.5__tar.gz → 2.5.7__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (40) hide show
  1. {toulligqc-2.5.5 → toulligqc-2.5.7}/PKG-INFO +1 -1
  2. {toulligqc-2.5.5 → toulligqc-2.5.7}/setup.py +3 -2
  3. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/fastq_extractor.py +4 -3
  4. toulligqc-2.5.7/toulligqc/version.py +1 -0
  5. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/PKG-INFO +1 -1
  6. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/requires.txt +2 -1
  7. toulligqc-2.5.5/toulligqc/version.py +0 -1
  8. {toulligqc-2.5.5 → toulligqc-2.5.7}/AUTHORS +0 -0
  9. {toulligqc-2.5.5 → toulligqc-2.5.7}/LICENSE-CeCILL.txt +0 -0
  10. {toulligqc-2.5.5 → toulligqc-2.5.7}/LICENSE.txt +0 -0
  11. {toulligqc-2.5.5 → toulligqc-2.5.7}/MANIFEST.in +0 -0
  12. {toulligqc-2.5.5 → toulligqc-2.5.7}/README.md +0 -0
  13. {toulligqc-2.5.5 → toulligqc-2.5.7}/setup.cfg +0 -0
  14. {toulligqc-2.5.5 → toulligqc-2.5.7}/test/test_sequencing_summary_extractor.py +0 -0
  15. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/__init__.py +0 -0
  16. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/bam_extractor.py +0 -0
  17. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/common.py +0 -0
  18. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/common_statistics.py +0 -0
  19. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/configuration.py +0 -0
  20. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/extractor_common.py +0 -0
  21. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/fast5_extractor.py +0 -0
  22. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/fastq_bam_common.py +0 -0
  23. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/html_report_generator.py +0 -0
  24. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/plotly_graph_common.py +0 -0
  25. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/plotly_graph_generator.py +0 -0
  26. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/plotly_graph_onedsquare_generator.py +0 -0
  27. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/report_data_file_generator.py +0 -0
  28. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/resources/plotly-latest.min.js +0 -0
  29. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/resources/toulligqc.css +0 -0
  30. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/resources/toulligqc.png +0 -0
  31. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/sequencing_summary_extractor.py +0 -0
  32. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/sequencing_summary_onedsquare_extractor.py +0 -0
  33. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/sequencing_telemetry_extractor.py +0 -0
  34. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/toulligqc.py +0 -0
  35. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/toulligqc_info_extractor.py +0 -0
  36. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/SOURCES.txt +0 -0
  37. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/dependency_links.txt +0 -0
  38. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/entry_points.txt +0 -0
  39. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/not-zip-safe +0 -0
  40. {toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/top_level.txt +0 -0
{toulligqc-2.5.5 → toulligqc-2.5.7}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: toulligqc
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- Version: 2.5.5
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+ Version: 2.5.7
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  Summary: A post sequencing QC tool for Oxford Nanopore sequencers
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  Home-page: https://github.com/GenomicParisCentre/toulligQC
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  Author: Genomic Paris Centre team
{toulligqc-2.5.5 → toulligqc-2.5.7}/setup.py RENAMED
@@ -46,9 +46,10 @@ setup(
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  include_package_data=True,
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  python_requires='>=3.11.0',
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- install_requires=['matplotlib>=3.6.3', 'plotly>=5.15.0', 'h5py>=3.7.0',
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+ install_requires=['matplotlib>=3.6.3', 'plotly==4.5.0', 'h5py>=3.7.0',
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  'pandas>=1.5.3', 'numpy>=1.24.2', 'scipy>=1.10.1',
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- 'scikit-learn>=1.2.1', 'tqdm>=4.64.1', 'pysam>=0.21.0'],
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+ 'scikit-learn>=1.2.1', 'tqdm>=4.64.1', 'pysam>=0.21.0',
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+ 'ezcharts==0.7.6'],
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  entry_points={
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  'console_scripts': [
{toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/fastq_extractor.py RENAMED
@@ -283,9 +283,10 @@ class fastqExtractor:
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  fastq_lines.append((len(read[1]), qscore, passes_filtering, start_time, ch))
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  else:
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  for read in read_batch:
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- qscore = avg_qual(read)
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- passes_filtering = True if qscore > self.threshold_Qscore else False
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- fastq_lines.append((len(read), qscore, passes_filtering))
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+ if len(read)>0:
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+ qscore = avg_qual(read)
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+ passes_filtering = True if qscore > self.threshold_Qscore else False
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+ fastq_lines.append((len(read), qscore, passes_filtering))
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  return fastq_lines
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toulligqc-2.5.7/toulligqc/version.py ADDED
@@ -0,0 +1 @@
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+ __version__ = '2.5.7'
{toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.1
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  Name: toulligqc
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- Version: 2.5.5
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+ Version: 2.5.7
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  Summary: A post sequencing QC tool for Oxford Nanopore sequencers
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  Home-page: https://github.com/GenomicParisCentre/toulligQC
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  Author: Genomic Paris Centre team
{toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc.egg-info/requires.txt RENAMED
@@ -1,8 +1,9 @@
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+ ezcharts==0.7.6
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  h5py>=3.7.0
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  matplotlib>=3.6.3
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  numpy>=1.24.2
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  pandas>=1.5.3
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- plotly>=5.15.0
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+ plotly==4.5.0
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  pysam>=0.21.0
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  scikit-learn>=1.2.1
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  scipy>=1.10.1
toulligqc-2.5.5/toulligqc/version.py DELETED
@@ -1 +0,0 @@
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- __version__ = '2.5.5'
{toulligqc-2.5.5 → toulligqc-2.5.7}/AUTHORS RENAMED
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{toulligqc-2.5.5 → toulligqc-2.5.7}/LICENSE-CeCILL.txt RENAMED
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{toulligqc-2.5.5 → toulligqc-2.5.7}/LICENSE.txt RENAMED
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{toulligqc-2.5.5 → toulligqc-2.5.7}/MANIFEST.in RENAMED
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{toulligqc-2.5.5 → toulligqc-2.5.7}/README.md RENAMED
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{toulligqc-2.5.5 → toulligqc-2.5.7}/setup.cfg RENAMED
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{toulligqc-2.5.5 → toulligqc-2.5.7}/toulligqc/common.py RENAMED
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