toulligqc 2.7__tar.gz → 2.8__tar.gz

toulligqc-2.8/.gitignore

@@ -0,0 +1,238 @@
+
+# Created by https://www.gitignore.io/api/git,python,pycharm,visualstudiocode
+# Edit at https://www.gitignore.io/?templates=git,python,pycharm,visualstudiocode
+
+### Git ###
+# Created by git for backups. To disable backups in Git:
+# $ git config --global mergetool.keepBackup false
+*.orig
+
+# Created by git when using merge tools for conflicts
+*.BACKUP.*
+*.BASE.*
+*.LOCAL.*
+*.REMOTE.*
+*_BACKUP_*.txt
+*_BASE_*.txt
+*_LOCAL_*.txt
+*_REMOTE_*.txt
+
+### PyCharm ###
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and WebStorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+
+# User-specific stuff
+.idea/**/workspace.xml
+.idea/**/tasks.xml
+.idea/**/usage.statistics.xml
+.idea/**/dictionaries
+.idea/**/shelf
+
+# Generated files
+.idea/**/contentModel.xml
+
+# Sensitive or high-churn files
+.idea/**/dataSources/
+.idea/**/dataSources.ids
+.idea/**/dataSources.local.xml
+.idea/**/sqlDataSources.xml
+.idea/**/dynamic.xml
+.idea/**/uiDesigner.xml
+.idea/**/dbnavigator.xml
+
+# Gradle
+.idea/**/gradle.xml
+.idea/**/libraries
+
+# Gradle and Maven with auto-import
+# When using Gradle or Maven with auto-import, you should exclude module files,
+# since they will be recreated, and may cause churn.  Uncomment if using
+# auto-import.
+# .idea/modules.xml
+# .idea/*.iml
+# .idea/modules
+# *.iml
+# *.ipr
+
+# CMake
+cmake-build-*/
+
+# Mongo Explorer plugin
+.idea/**/mongoSettings.xml
+
+# File-based project format
+*.iws
+
+# IntelliJ
+out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Cursive Clojure plugin
+.idea/replstate.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+
+# Editor-based Rest Client
+.idea/httpRequests
+
+# Android studio 3.1+ serialized cache file
+.idea/caches/build_file_checksums.ser
+
+### PyCharm Patch ###
+# Comment Reason: https://github.com/joeblau/gitignore.io/issues/186#issuecomment-215987721
+
+# *.iml
+# modules.xml
+# .idea/misc.xml
+# *.ipr
+
+# Sonarlint plugin
+.idea/**/sonarlint/
+
+# SonarQube Plugin
+.idea/**/sonarIssues.xml
+
+# Markdown Navigator plugin
+.idea/**/markdown-navigator.xml
+.idea/**/markdown-navigator/
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+# for local use
+__main__.py
+
+# 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
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv
+# .python-version (commented out as uv uses this file)
+
+# uv
+uv.lock
+.venv/
+
+# 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
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+### VisualStudioCode ###
+.vscode/*
+.vscode/settings.json
+!.vscode/tasks.json
+.vscode/launch.json
+!.vscode/extensions.json
+
+### VisualStudioCode Patch ###
+# Ignore all local history of files
+.history
+
+ ### Ignore test directory
+ test/
+
+ ### Ignore other files put to test_data/
+
+/test_data
+
+
+# End of https://www.gitignore.io/api/git,python,pycharm,visualstudiocode

toulligqc-2.8/CHANGES.md

@@ -0,0 +1,215 @@
+# Changelog
+
+## 2.8 (2025-02-04)
+* Now use uv to build the project.
+* Demo scripts are now in the GitHub repository.
+* Add a new command line option `--use-aliases-for-barcodes`, to use the "alias" column in sample sheet instead of the "barcode" column.
+* Fix issue #44, the name of the first column of the sequencing summary file has changed with new Nanopore specification.
+
+## 2.7.1 (2024-08-23)
+* Added Conda environment.yml.
+* Fixed bugs:
+  * Corrected N50 and L50 computation (issue #28).
+  * Recognized the standard barcode arrangement (BC|RB|NB|BP) in the samplesheet (issue #27).
+  * Fixed barcoding for the Fastq_extractor (issue #30).
+  * Fixed time format for BAM and FASTQ extractors.
+  
+
+## 2.7 (2024-06-21)
+* Moved to Ubuntu 24.04.
+* Added support for ONT samplesheet.
+* ToulligQC now recognizes the barcode column name as 'barcode'.
+* ToulligQC now supports irregular barcode naming; issue #22.
+* Fixed bugs:
+  * Pandas inplace issue for FASTQ and onedsquare summary files.
+  * PlotlyJS inclusion for independent image exports.
+  * Corrected read/base count histogram.
+  * Handled empty lines in FASTQ file.
+  * Resolved compression issue in pod5 file.
+  * BAM extractor can now deal with any BAM, even if it has not been generated by Dorado.
+  * Handled barcode name when it's associated with kit_barcode.
+
+## 2.6 (2024-01-26)
+* Support for the POD5 format.
+* Handling of barcoding in BAM and FASTQ files.
+* Support for Fast5 .tar files without compression.
+* Fixed an issue with BAM tags extraction.
+* Fixed the issue with the 'passes_filtering'-only sequencing summary.
+* Fixed the bug related to numpy.bool with numpy version 1.24 or later.
+* Improved compatibility with pandas 2.0.
+
+## 2.5 (2023-11-03)
+* Fixed error when no failed reads were found (Issue #20).
+* Fixed error when unclassified barcodes were missing.
+* FASTQ and BAM files can now be used instead of the sequencing summary file.
+* Added the ability to specify a barcode range (e.g., `--barcodes barcode01:barcode48`).
+
+## 2.4 (2023-04-26)
+* In over time graphs (read length, PHRED score and translocation speed), now fill the gaps for the 75% and 25% to avoid filling glitch.
+* Fix 2D density plot title style.
+* Fix error when a summary file with barcode information was provided in addition of barcoding files (Issue #17), now the barcode files will be skipped with a warning message in case summary file with barcode information is provided.
+* Add the selected speed and sample frequency of the run in the "Run statistics" table of the ToulligQC report
+
+## 2.3 (2023-03-22)
+* Numpy 1.24 is now supported (thanks to Sean Black).
+* Scatter plot of read length vs PHRED score has been replaced by a 2D density plot.
+* Add bases per barcode distribution graphs.
+
+## 2.2.3 (2022-09-29)
+* Fix error when no Fast5 file is found in a directory provided as argument. Now throw an understandable error message.
+
+## 2.2.2 (2022-08-31)
+* Fix when multiple sequencing summary barcode files were available, the type of the 'barcode_arrangement' column in the dataframe was not correct.
+
+## 2.2.1 (2022-01-05)
+* Generated images were not included in the main HTML report file.
+
+## 2.2 (2022-01-03)
+* Add some flexibility to barcode specification (Thanks to  Hunter Cameron).
+* The sequencing_summary.txt and sequencing_telemetry.js files can now be read compressed in gzip or bzip2.
+* Add some log information on stdout for duration of the sequencing summary extractors.
+* Change the format of the duration in log.
+* Now logs memory used by dataframes.
+* Fix Docker image build issue when updating setuptools.
+* QScores and durations are now stored in 32 bits floats instead of 64 bits to reduce memory consumption (≈25% for 1D data).
+* Barcode arrangements are now stored as categories instead of strings.
+
+## 2.1.1 (2021-08-18)
+* Fix issue when barcode list argument contains non existing barcode(s) in input data or when all existing barcodes are used.
+
+## 2.1 (2021-06-28)
+* The channel occupancy of the flowcell graph code has been rewritten to use Plotly. Add all/pass/fail/fail ratio views. The flowcell graph can now also handle Flongle and PromethION flowcels in addition of standard MinION flowcell
+* Add "Sequencing kit" and "Barcode kits" entries in the run statistics table in html report
+* In the distribution of read lengths graph, add buttons to show base count distribution in linear/log modes.
+* Fix scatterplot graph where the default max x-axis value was always the max value for fail reads
+* Fix help links in demo report
+* Fix the name of the "Device and software" and "Run statistics" sections
+
+## 2.0.1 (2021-04-14)
+* In setup.py, set the developement status for ToulligQC as Production/Stable instead of Beta
+* Add MANIFEST.in file to add resources files in PyPi package
+* Fix error with latest versions of NumPy by add a missing int casting
+
+## 2.0 (2021-04-09)
+* Fix duration computation
+* For PHRED score distribution boxplots, remove unnecessary interpolation before creating boxplot
+* Remove duplicated code for 1D and 1D2 in PHRED score distribution graphs
+* Remove duplicated code for 1D and 1D2 in Correlation between read length and PHRED score graphs
+* In read length distribution graphs, add buttons to switch between linear and log scale for xaxis
+* Add minimal qscore threshold in the "Device and software information" report table
+* In 1D/1D2 sequencing summary extractors, now replace NA values for barcode assignment by "unclassified". Print a warning message on console
+* Update unit tests
+* For read count histogram tables, replace "frequency" by "percent"
+* Rename y-axis for "Distribution of read lengths" graphs to "Read count"
+* Add new command line options to finely define output file paths 
+* Update the sigma value for gaussian filters when smoothing plots
+* In correlation scatterplots, now ponderate the number of pass/fail spots by the pass/fail ratio when using interpolation
+
+## 2.0b3 (2021-03-22)
+* New CSS for HTML report
+* Add new plots (Read length and PHRED over time, translocation speed...)
+* Enhancement of existing graphs
+* Big refactoring code for sequencing summary file parsing
+* Big refactoring code for creating plots
+* Reduce memory usage and execution time with barcodes
+* Fix Plotly dependency version requirement
+* Add L50 computation
+* Sequence lengths of reads was stored into np.int16 that cannot handle >=32kb reads. Now use np.uint32
+* Add ToulligQC logo in HTML report
+* A telemetry file or Fast5 file is no more required
+* Add new fields in the two first tables of the report: Run ID, operating system and basecalling date
+* Barcode distribution pie charts can now be visualised as histograms
+* In table, float values have now comma separator for thousands
+* Update the yield number format in run statistocs table
+* Update colors in the graphs
+* Add an information link in all the graph titles
+
+## 2.0b2 (2020-11-20)
+* Fix import bug
+* Fix graph names partially hidden in HTML summary element
+* Rewrite help and rename arguments for clarity
+* Create required and optional argument groups
+* Create default values for --report-name and --output command line arguments
+* Update report.html example in Docs with the new version of ToulliQC
+* Create new presentation image for README
+
+## 2.0b1 (2020-11-17)
+* Refactoring of the sequencing_summary_extractor
+* Refactoring of the 1dsqr_sequencing_summary_extractor
+* Many performance improvements (reducing memory usage)
+* Graphs are now made with Plotly
+* Removal of unused options (Albacore log, FASTQ files, configuration file and samplesheet file)
+* N50 information added to report.html
+* Removal of Albacore support
+* Now handle PromethION data
+* Update of required dependencies versions
+* Add unit tests
+* Add new plots (throughput sequencing time)
+* Update graph colors
+
+## 1.3 (2019-11-07)
+* Add a --barcodes option that allow to avoid samplesheet file creation
+* The size of the graphs are now set to 1000x600px
+* Many small fixes in graph generation (remove titles, fix grids and layouts...)
+* In the HTML report, replace the tooltip icon by an unicode character
+
+## 1.2 (2019-07-25)
+* MultiFast5 file can now be used to retrieve run information
+* Reporting other barcodes in the "other" category
+* Gathering information from Telemetry files in the HTML report
+
+## 1.1 (2019-03-21)
+* Add Guppy support for 1D and 1D2
+* Telemetry files generated by Albacore or Guppy can now be used to retrieve run information instead of reading a FAST5 file and the pipeline.log file.
+* Refactoring of the code of the extractors
+
+## 1.0 (2018-10-23)
+* Report.data log file reviewed
+
+## 0.10 (2018-07-18)
+* Add pipeline.log parsing option
+
+## 0.9 (2018-03-21)
+* Fix out of memory error when parsing big FASTQ files. The parsing of FASTQ files is now faster
+
+
+## 0.8 (2018-03-14)
+* Fix unexisting import in toulligqc.py
+* Fix the not working "--quiet" option
+
+
+## 0.7 (2018-03-14)
+* Fix Dockerfile that used the Ubuntu 17.04 (Ubuntu 17.04 packages repository is no more available)
+
+
+## 0.6 (2018-03-12)
+* Update html.report for 1D and 1Dsquare data
+* Fix issue when processing fast5 files directory
+* Add pass/fail filter
+* Add extractor and graphs for 1dsquare analysis
+
+
+## 0.5 (2017-11-28)
+* Fix exception when toulligqc was launched with no arguments
+* Remove pypandoc dependency in setup.py
+* Fix issue when checking if directory paths ends with a '/'
+* Fix issue when checking missing arguments
+
+
+## 0.4 (2017-11-27)
+* Fix issue with the --version option of ToulligQC
+
+
+## 0.3 (2017-11-27)
+* Fix issue with setup.py and pip install
+
+
+## 0.2 (2017-11-27)
+* ToulligQC can now handle Albacore 2.0 output
+* The run date is now extracted from a FAST5 file
+* Update setup.cfg for PyPi package submission
+* Update ToulligQC documentation
+
+
+## 0.1 (2017-08-30)
+* Initial version