Feature/release 2.0

.github/workflows/dependency-review.yml

@@ -10,14 +10,9 @@
 name: 'Dependency review'
 on:
   pull_request:
-    branches: [ "master" ]
+    branches:
+      - master # Triggers only on pull requests targeting the master branch
 
-# If using a dependency submission action in this workflow this permission will need to be set to:
-#
-# permissions:
-#   contents: write
-#
-# https://docs.github.com/en/enterprise-cloud@latest/code-security/supply-chain-security/understanding-your-software-supply-chain/using-the-dependency-submission-api
 permissions:
   contents: read
   # Write permissions for pull-requests are required for using the `comment-summary-in-pr` option, comment out if you aren't using this option
@@ -36,4 +31,4 @@ jobs:
           comment-summary-in-pr: always
         #   fail-on-severity: moderate
         #   deny-licenses: GPL-1.0-or-later, LGPL-2.0-or-later
-        #   retry-on-snapshot-warnings: true
+        #   retry-on-snapshot-warnings: true

.github/workflows/lint.yml

@@ -0,0 +1,53 @@
+# This is a GitHub Actions workflow file for linting Python code using Tox and Flake8.
+name: Lint
+
+on:
+  push:
+    branches:
+      - '**'  # run on every push to any branch
+  pull_request:
+    branches:
+      - master  # run on pull requests targeting the master branch
+
+permissions:
+  contents: write
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      # Step 1: Checkout the repository
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0  # Fetch the full history to allow branch checkout
+
+      # Step 2: Determine the branch name
+      - name: Get branch name
+        id: vars
+        run: |
+          if [ "${{ github.event_name }}" = "pull_request" ]; then
+            echo "BRANCH_NAME=${{ github.head_ref }}" >> $GITHUB_ENV
+          else
+            echo "BRANCH_NAME=$(echo ${GITHUB_REF#refs/heads/})" >> $GITHUB_ENV
+          fi
+
+      # Step 3: Install dependencies
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install tox
+
+      # Step 4: Run Tox for Linting
+      - name: Run Tox Lint
+        run: tox -e flake8
+
+      # Step 5: Commit and push changes if Black reformats files
+      - name: Commit and push changes
+        run: |
+          git config --global user.name "GitHub Actions"
+          git config --global user.email "[email protected]"
+          git checkout $BRANCH_NAME  # Check out the branch
+          git add .
+          git commit -m "Apply linting fixes" || echo "No changes to commit"
+          git push origin $BRANCH_NAME

.github/workflows/tests.yml

@@ -10,7 +10,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.10', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v2

.readthedocs.yaml

@@ -8,6 +8,6 @@ sphinx:
 
 # Explicitly set the version of Python
 python:
-  version: 3.8
+  version: 3.12
   install:
     - requirements: docs/requirements.txt

CHANGELOG.md

@@ -1,24 +1,40 @@
 # Change Log
 
 ## TODO: ideas, issues and planed extensions or changes that are not yet implemented
+
 * optimize add_qc_metrics for run after new samples have been added - should not recompute everything
-* planned new feature: during import of long reads, (optionally) correct for short exon alignment issues. 
+* planned new feature: during import of long reads, (optionally) correct for short exon alignment issues.
 * separate new read import and classification of isoforms.
 
+## [2.0.0]
+
+* support the analysis of Oxford Nanopore data
+* new option of TSS identification according to the reference annotation
+* new gene model characteristics, simplex coordinates and relative entropy
+* new visualisation using triangle plot
+* fix bugs in external gtf import to reconstruct transcriptome
+* improve the coordination analysis of TSS and PAS
+* support the import of SQANTI QC report and filtering based on it
+* support the export of positive and negative TSS for ML
+* support proteogenomic approaches at the interface of transcriptomics and proteomics
+* improve code readability and filter tag construction
+
 ## [0.3.5]
+
 * fixed a bug in domain plots, which was introduced in 0.3.4
 * fixed a bug in iter_genes/iter_transcripts with region='chr', and no positions specified
 * new option in plot_domains to depict noncoding transcripts, controlled with the coding_only parameter
 
 ## [0.3.4]
+
 * fixing #8: AssertationError when unifying TSS/PAS between transcript
-* improved domain plots: ORF start and end do not appear like exon exon boundaries. 
-* API change: separated ORF prediction from QC metrics calculation. 
+* improved domain plots: ORF start and end do not appear like exon exon boundaries.
+* API change: separated ORF prediction from QC metrics calculation.
 * new feature: count number of upstream start codons in Gene.add_orfs() (called by default when adding QC metrics to transcriptome)
-* new feature: calculate Fickett testcode and hexamer score for longest ORFs, to separate coding and noncoding genes. 
-
+* new feature: calculate Fickett testcode and hexamer score for longest ORFs, to separate coding and noncoding genes.
 
 ## [0.3.3]
+
 * fixed bug in filter_ref_transcripts with no query
 * export gtf with long read transcripts as well uncovered as reference transcripts
 * fix warning in plot_diff_results
@@ -28,11 +44,13 @@
 * improved documentation: syntax highlighting, code style, additional explanations on filtering
 
 ## [0.3.2]
+
 * restructured tutorials
 * new feature: add domains to differential splicing result tables.
 * new feature: min_coverage and max_coverage for iter_genes function.
 
 ## [0.3.1]
+
 * new feature: add protein domains from 3 different sources and depict them with Gene.plot_domains()
 * new feature: restrict gene and transcript iterators on list of genes of interest
 * new feature: filter_transcripts function for genes
@@ -43,39 +61,45 @@
     * order of events is now according to gene strand: A upstream of B
 
 ## [0.3.0]
+
 * new feature: find longest ORF and infer NMD of lr transcripts (and annotation)
 * new feature: allow for several TSS/PAS per intron chain and unify them across intron chains
 * changed default parameter of filter_query in run_isotools script to "FSM or not (INTERNAL_PRIMING or RTTS)"
 
 ## [0.2.11.1]
-* bugfix: KeyError during transcriptome reconstruction in _add_chimeric. 
+
+* bugfix: KeyError during transcriptome reconstruction in _add_chimeric.
 * bugfix: default colors in plot_diff_results.
 
 ## [0.2.11]
+
 * added function to import samples from csv/gtf to import transcriptome reconstruction / quantification from other tools.
 * dropped requirement for gtf files to be tabix indexed.
 
 
 ## [0.2.10]
+
 * fixed get_overlap - important for correct assignment of mono exonic genes to reference
 * added parameter to control for minimal mapping quality in add_sample_from_bam. This allows for filtering out ambiguous reads, which have mapping quality of 0
 * fixed plot_diff_result (Key error due to incorrect parsing of group names)
-* New function estimate_tpm_threshold, to estimate the minimal abundance level of observable transcripts, given a sequencing depth. 
-* New function coordination_test, to test coordination of splicing events within a gene. 
+* New function estimate_tpm_threshold, to estimate the minimal abundance level of observable transcripts, given a sequencing depth.
+* New function coordination_test, to test coordination of splicing events within a gene.
 * Optional log or linear scale for the coverage axis in sashimi plots.
 
 ## [0.2.9]
+
 * added DIE test
 * adjusted classification of novel exonic TSS/PAS to ISM
-* improved assignment of reference genes in case of equal number of matching splice sites to several reference genes. 
+* improved assignment of reference genes in case of equal number of matching splice sites to several reference genes.
 * added parameter to control for minimal exonic overlap to reference genes in add_sample_from_bam.
 * changed computation of direct repeats. Added wobble and max_mm parameters.
-* exposed parameters to end user in the add_qc_metrics function. 
+* exposed parameters to end user in the add_qc_metrics function.
 * added options for additional fields in gtf output
 * improved options for graphical output with the command line script
 * fixed plot_bar default color scheme
 
 ## [0.2.8]
+
 * fix: version information lost when pickeling reference.
 * fix missing gene name
 * added pt_size parameter to plot_embedding and plot_diff_results function
@@ -84,11 +108,13 @@
 
 
 ## [0.2.7]
+
 * added command line script run_isotools.py
-* added test data for unit tests 
+* added test data for unit tests
 
 
 ## [0.2.6]
+
 * Added unit tests
 * Fixed bug in novel splicing subcategory assignment
 * new feature: rarefaction analysis
@@ -98,55 +124,63 @@
     * added optional progress bar to iter_genes/transcripts
 
 ## [0.2.5]
+
 * New feature: distinguish noncanonical and canonical novel splice sites for direct repeat hist
 * New feature: option to drop partially aligned reads with the min_align_fraction parameter in add_sample_from_bam
 
 ## [0.2.4]
+
 * New feature: added option to save read names during bam import
 * new feature: gzip compressed gtf output
 
 ## [0.2.3]
+
 * Changed assignment of transcripts to genes if no splice sites match.
 * Fix: more flexible import of reference files, gene name not required (but id is), introducing "infer_genes" from exon entries of gtf files.
 * New function: Transcriptome.remove_filter(filter=[tags])
 
 ## [0.2.2]
+
 * Fix: export to gtf with filter features
 
 ## [0.2.1]
+
 * Fix: import reference from gtf file
 * New feature: Import multiple samples from single bam tagged by barcode (e.g. from single cell data)
 * Fix: issue with zero base exons after shifting fuzzy junctions
 
-
 ## [0.2.0]
+
 * restructure to meet PyPI recommendations
 * New feature: isoseq.altsplice_test accepts more than 2 groups, and computes ML parameters for all groups
 
 ## [0.1.5]
+
 * New feature: restrict tests on provided splice_types
 * New feature: provide position to find given alternative splicing events
 
 ## [0.1.4]
+
 * Fix: Issue with noncanonical splicing detection introduced in 0.1.3
 * Fix: crash with secondary alignments in bam files during import.
 * New feature: Report and skip if alignment outside chromosome (uLTRA issue)
 * Fix: import of chimeric reads (secondary alignments have no SA tag)
-* Fix: Transcripts per sample in sample table: During import count only used transcripts, do not count chimeric transcripts twice. 
+* Fix: Transcripts per sample in sample table: During import count only used transcripts, do not count chimeric transcripts twice.
 * Change: sample_table reports chimeric_reads and nonchimeric_reads (instead of total_reads)
 * Change: import of long read bam is more verbose in info mode
 * Fix: Bug: import of chained chimeric alignments overwrites read coverage when merging to existing transcript
 * Fix: remove_samples actually removes the samples from the sample_table
 * Change: refactored add_biases to add_qc_metrics
 * fix: property of transcripts included {sample_name:0}
 * save the TSS and PAS positions
-* New: use_satag parameter for add_sample_from_bam 
+* New: use_satag parameter for add_sample_from_bam
 * Change: use median TSS/PAS (of all reads with same splice pattern) as transcript start/end (e.g. exons[0][0]/exons[-1][1])
 * Fix: Novel exon skipping annotation now finds all exonic regions that are skipped.
 * change: Default filter of FRAGMENTS now only tags reads that do not use a reference TSS or PAS
+
 ## [0.1.3]
-* Fix: improved performance of noncanonical splicing detection by avoiding redundant lookups. 
 
+* Fix: improved performance of noncanonical splicing detection by avoiding redundant lookups.
 
 ## [0.1.2] - 2020-05-03
 
@@ -157,7 +191,6 @@
 * New: Do not distinguish intronic/exonic novel splice sites. Report distance to shortest splice site of same type.
 * Fix: Sashimi plots ignored mono exons
 
-
 ## [0.1.1] - 2020-04-12
 
 * Fix: fixed bug in TSS/PAS events affecting start/end positions and known flag.
@@ -170,23 +203,23 @@
 * moved examples in documentation
 
 ## [0.0.2] - 2020-03-22
+
 * Change: refactored SpliceGraph to SegmentGraph to better comply with common terms in literature
-* New: added a basic implementation of an actual SpliceGraph (as commonly defined in literature) 
+* New: added a basic implementation of an actual SpliceGraph (as commonly defined in literature)
     * based on sorted dict
     * not used so far, but maybe useful in importing the long read bam files since it can be extended easily
-* New: added decorators "experimental" and "deprecated" to mark unsafe functions 
+* New: added decorators "experimental" and "deprecated" to mark unsafe functions
 * Change: in differential splicing changed the alternative fraction, to match the common PSI (% spliced in) definition
 * Change: narrowed definition of mutually exclusive exons: the alternatives now need to to feature exactly one ME exon and rejoin at node C
 * Change: for ME exons now the beginning of node C is returned as "end" of the splice bubble
-* New: differential splicing result contains "novel", indicating that the the alternative is in the annotation 
+* New: differential splicing result contains "novel", indicating that the the alternative is in the annotation
 * New: added alternative TSS/alternative PAS to the differential splicing test
 * Change: removed obsolete weights from splice graph and added strand
 * Change: unified parameters and column names of results of Transcriptome.find_splice_bubbles() and Transcriptome.altsplice_test()
-* Fix: add_short_read_coverage broken if short reads are already there. 
-
+* Fix: add_short_read_coverage broken if short reads are already there.
 
 ## [0.0.1] - 2020-02-25
+
 * first shared version
 * New: added option to export alternative splicing events for MISO and rMATS
 * New: added change log
-

README.md

@@ -62,5 +62,7 @@ isoseq.save('../tests/data/example_1_isotools.pkl')
 ## Citation and feedback:
 
 * If you run into any issues, please use the [github issues report feature](https://github.com/HerwigLab/IsoTools2/issues).
-* For general feedback, please write me an email to [[email protected]](mailto:[email protected]).
-* If you use IsoTools in your publication, please cite the following [paper](https://doi.org/10.1093/bioinformatics/btad364): Lienhard et al, Bioinformatics, 2023: IsoTools: a flexible workflow for long-read transcriptome sequencing analysis
+* For general feedback, please write us an email to [[email protected]](mailto:[email protected]) and [[email protected]](mailto:[email protected]).
+* If you use IsoTools in your publication, please cite the following paper in addition to this repository:
+  * Lienhard, Matthias et al. “IsoTools: a flexible workflow for long-read transcriptome sequencing analysis.” Bioinformatics (Oxford, England) vol. 39,6 (2023): btad364. [doi:10.1093/bioinformatics/btad364](https://doi.org/10.1093/bioinformatics/btad364)
+  * Bi, Yalan et al. “IsoTools 2.0: Software for Comprehensive Analysis of Long-read Transcriptome Sequencing Data.” Journal of molecular biology, 169049. 26 Feb. 2025, [doi:10.1016/j.jmb.2025.169049](https://doi.org/10.1016/j.jmb.2025.169049)

VERSION.txt

@@ -1 +1 @@
-0.3.5_rc11
+2.0.0