v5.3.6

What's Changed

• Update sqanti3_filter.py by @sbresnahan in #397
• Updated the fl count parser to accept floats in single samples by @pabloati in #406
• Input file processing upgraded to accept any kind og GTF by @pabloati in #407
• Fixed report to accept classification with junction types missing by @pabloati in #408
• Issue 390, pallete and flair input fixed by @pabloati in #412
• GMST directory saved after parallelization by @pabloati in #414
• Release 5.3.6 update by @pabloati in #415

New Contributors

• @sbresnahan made their first contribution in #397

Full Changelog: v5.3.5...v5.3.6

v5.3.5

What's Changed

• Reduced the strictness for the arguments in SQANTI QC
• Fixed temporary files removal in parallelization as in issue 388
• Fixed subclassification of NIC between intergenic and genic intron as in issue 389
• update to reach master and make changes by @carolinamonzo in #393
• Sqanti reads devel updating utilities paths by @carolinamonzo in #394
• Updated example and tests to match the new improvements

Full Changelog: v5.3.4...v5.3.5

Release 5.3.4: Classification and subclassfication bug fixes

Through there release, the main issues fixed are related to the issues 381 and 379. As new features, SQANTI3 directly takes one bam file as SR_bam input, and the input format for the isoforms ID has been expanded to accept non-IsoSeq nomenclature.

What's Changed

• SR_bam now parses bam files directly by @pabloati in #383
• Updated the isoform sorting to accept a wider nomenclature by @pabloati in #384
• Fixed subclassification bug for NNC by @pabloati in #385
• changed the input gtf to output introns to the corrected cds gff by @CarlosBlancoGo in #370
• Sqanti reads devel merge compatibility fix from Carlos by @carolinamonzo in #386

New Contributors

• @CarlosBlancoGo made their first contribution in #370

Full Changelog: v5.3.3...v5.3.4

Release 5.3.3: GMST and dependencies bugs fixing

This release fixes an error where the HMM from GeneMarkS-T was saved in the script where SQANTI3 was being called. This caused issues when the parallelization was run, since the HMMs from different chunks tried to overwrite each other. Some minor changes were made to fix deprecated dependencies and versioning

What's Changed

• Fixed GMST so the HMM is saved in its directory by @pabloati in #380
• Updated deprecated dependencies (shutil to search for executables)
• Unified the versioning system

Full Changelog: v5.3.2...v5.3.3

Release 5.3.2: Parallelization and classification bug fixes

This release is focused on fixing three known bugs in SQANTI3 qc. Firstly it fixes a bug that caused some transcripts that should be classified as genic introns to be intergenic. Another bug was related to the CAGE peaks and determining the distance to the TSS. Finally, the main issue was in the paralleliztaion, where different results were being obtained for the associated gene name, the RT switching and the FSM classification. Furthermore, RT switching had a bug, where only one junction from all the ones that were the same was being saved in the output file as having the RT switching event, and thus only some isoforms had it too.

Whats new

• Minor code changes for readibility
• Fixed genic intron classification bug by @pabloati from #374
• Fixed CAGE peaks bug by @alexpan00
• Revamp and bug fixing of the paralellization by @pabloati from #340
• RT switching bug fixed by @pabloati from #197

Full Changelog: v5.3.1...v5.3.2

Release 5.3.1: SQANTI3 QC revamp

This release only changes the structure of SQANTI3 QC, not adding any new functionality. Now, the sqanti3_qc.py script has been divided into different modules under the src directory, to facilitate the creation of a test suite and debugging. These division has been done on following a functionality logic, where functions that serve the same purpose have are part of the same module (such as parsers, classes or the classifying functions).

As well, an initial test suite has been developed, that can be directly executed running pytest from the command line while being inside of the main directory of SQANTI3

New Contributors

• @pabloati made their first contribution to develop this release

Full Changelog: v5.3.0...v5.3.1

SQANTI 5.3.0

This release include some new minor features, such as the inclusion of a Dockerfile of sqanti and a wrapper to execute all SQANTI steps at once. Also enhances compatibility for fastq.gz files in sqanti3_qc.py and a new sqanti tool, sqanti_reads.py!

Several bugfixes are corrected: Sqanti QC report is now more robust in absence of some categories of transcripts and transcripts with unknown strands are redirected to an external file to inform the user about possible problems. Full list of changes is below

What's Changed

• Sqanti reads by @carolinamonzo in #321
• Dockerfile by @Fabian-RY in #323
• Added compatibility for .gz compressed fasta/fastq isoforms to SQANTI3_QC by @Fabian-RY in #326
• Fixes report failing when some some structural categories (mainly FSM, ISM, NIC or NNIC) were missing by @Fabian-RY in #332
• Add NA replacement value for ratio_TSS column in ML Rescue by @aarzalluz in #330
• FIX: corrected unchecked existance of a variable in report when --skipORF is used by @Fabian-RY in #339
• FIX: transcripts without known strands (with '.' strand) are redirected by @Fabian-RY in #336
• Bugfix: corrected the sign in difference to TTS/TSS by @Fabian-RY and @alexpan00 in #337
• FIX: gtf.cds.gff is now created when --chunks options is used by @Fabian-RY in #341
• Sqanti3 wrapper available by @Fabian-RY in #344
• Fix: TSS and TTS now is corrected and documented by @Fabian-RY and @alexpan00 in #345
• Sqanti reads devel by @carolinamonzo in #356
• Fixing stuff for paper revision by @carolinamonzo in #358
• Sqanti reads devel updating environment by @carolinamonzo in #359

New Contributors

• @Fabian-RY made their first contribution in #323

Full Changelog: v5.2.2...v5.3.0

SQANTI3 v5.2.2

Since the latest release, improvements in genic intron e7054ab intergenic and NIC isoform classification have been included a7c2680 Errors in the conda environment generation have been solved and monoexons that don't overlap an entire junction will be considered genic, not NIC. Only when the monoexon spans a whole intron will be considered NIC by intron retention 3275a7f. Also CAGE peak assignation has been improved 52def33.

SQANTI3 v5.2.1

Release Update
We're excited to announce this release, bringing crucial fixes and enhancements to improve your experience:

Bug Fixes:

• Resolved a fatal error in SQANTI3 report generation (Issue #278).
• Resolved the issue with the missing 'howtouse.png' image in the HTML report.

Enhancements:

• Simplified installation by removing the cDNA_Cupcake dependency, thanks to @diekhans (Issue #271).
• Fixed issues with reading STAR junction/coverage files in Squanti3 V 5.2 through update conda environment (Issue #260).
• Corrected an error in generating the Kallisto index through update conda environment (Issue #257).

These updates aim to streamline your workflow and enhance software reliability. We thank our community for their valuable input and support.

SQANTI3 v5.2

Update sqanti3_rescue.py version