Update Pipelines

Updated all pipelines wrt set selection options.

What's Changed

• Correct set size option by @IsraMekki0 in #110

Full Changelog: v1.0.0...v1.0.1

Modularized version of Oligo Designer Toolsuite

Major Release:

We refactored the whole code into a modular version and implemented four ready to use probe design pipeline.

The modularized version now allows to plug different processing steps together to implement new oligo design pipelines eifficently. Furthermore, we have an underlying data structure that connects all modules via the same API. The new modules decsribe the different processing steps of oligo design pipeline, i.e. Property Filters, Specificity Filters, Scorings and Set Selection.

The new pipelines are: Scrinshot (modularized), Merfish, SeqFish+ and Oligo-Seq experiments

We also added tests for all implemented functionalities as well as integration tests for each pipeline, included into GitHub Actions.

In addition, we added an exhaustive documentation on the framework, installation, how to build custom pipelines and each offered ready to use pipeline.

What's Changed

• Add functionality to _ftp_loader.py by @chelseabright96 in #8
• Add functionality to data_parser.py by @chelseabright96 in #10
• Pre filters by @francesco-campi in #12
• Unit tests by @francesco-campi in #13
• Probesets by @francesco-campi in #15
• Update README.md by @francesco-campi in #17
• Joblib by @chelseabright96 in #14
• Padlock pipeline by @francesco-campi in #19
• docs update by @francesco-campi in #20
• Test docs by @IsraMekki0 in #21
• Databse split by @francesco-campi in #22
• Tutorial fix by @francesco-campi in #23
• Refactoring by @lisa-sousa in #24
• Padlock pipeline by @francesco-campi in #25
• Gff parser fix by @francesco-campi in #29
• Feature/new property filters by @IsraMekki0 in #33
• Cross hybrid by @IsraMekki0 in #35
• Feature/refactor property filter by @lisa-sousa in #37
• Database refactor by @lisa-sousa in #36
• Feature/refactor_property_filter by @francesco-campi in #38
• Update specificity by @IsraMekki0 in #34
• 39 integrate exact match filter into cross hybridization filter by @lisa-sousa in #48
• Bugfix/test errors by @IsraMekki0 in #45
• AI-filters by @francesco-campi in #54
• 49 exact match filter by @lisa-sousa in #55
• 46 oligo database attributes class by @lisa-sousa in #51
• Changed instances of dictionaries to LRUDDBDict by @IsraMekki0 in #56
• Update tests by @IsraMekki0 in #57
• 52 oligo scoring functions by @lisa-sousa in #60
• Oligo-seq-pipeline by @francesco-campi in #63
• 53 scrinshot pipeline by @lisa-sousa in #64
• Implemented heterodimer filter by @IsraMekki0 in #65
• Enhance database loading by @lisa-sousa in #67
• remove Bio package for blast and turn into subprocess by @lisa-sousa in #68
• 62 seqfish pipeline by @lisa-sousa in #78
• 69 filter for isoform consensus by @lisa-sousa in #73
• 71 utr sequence by @lisa-sousa in #74
• 75 exon junction computation by @lisa-sousa in #76
• 72 database table output by @lisa-sousa in #85
• 77 filter for exon number by @lisa-sousa in #79
• 81 intergenic sequence computation by @lisa-sousa in #84
• 80 update pytests by @lisa-sousa in #87
• Faster heuristic method to generate non-overlapping sets by @IsraMekki0 in #86
• Start split tutorial (1-4) by @IsraMekki0 in #90
• Add links in doc by @IsraMekki0 in #91
• 82 documentation by @lisa-sousa in #88
• 89 refactor pipelines by @lisa-sousa in #92
• New version of Oligo Designer Toolsuite by @IsraMekki0 in #93
• Docs by @IsraMekki0 in #95
• Update README.md by @lisa-sousa in #97

New Contributors

• @chelseabright96 made their first contribution in #8

Full Changelog: v0.1.3...v1.0.0

v0.1.3 - first release

First release of oligo-designer-toolsuite implementing the Padlock probe design pipeline for human and mouse species.