CHANGELOG.md

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.
• separate new read import and classification of isoforms.

[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.
• 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.

[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
• changed export to rMATS: events report complete flanking exons of top covered isoform
• fixed bug with transcript_id_col parameter in add_sample_from_csv
• fixed handling of interpro protein domains
• 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
• changed SUBSTANTIAL filter to 1% of the genes total (was 5%)
• coordination test:
  • changed argument and column naming, to make it consistent with other test results
  • added conditional delta PSI effect size measure
  • 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: 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.
• 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.
• 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.
• 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
• added colors parameter to plotting functions
• various fixes of command line script run_isotools.py

[0.2.7]

• added command line script run_isotools.py
• added test data for unit tests

[0.2.6]

• Added unit tests
• Fixed bug in novel splicing subcategory assignment
• new feature: rarefaction analysis
• Changed filtering: expressions get evaluated during iteration
  • Predefined filters are added automatically
  • Add / remove filters one by one
  • 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.
• 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
• 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.

[0.1.2] - 2020-05-03

• New: added function remove_short_read_coverage
• New: added some missing documentation for gene plots
• Fix: fixed bug in novel transcript class definition, affecting last exons
• New: Distinguish novel exonic TSS (NIC) and novel intronic TSS (NNC)
• 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.
• Change: refactored Transcriptome.find_splice_bubbles() to Transcriptome.alternative_splicing_events()
• Change: refactored SegmentGraph.find_alternative_starts() to SegmentGraph.find_start_end_events()

[0.1.0] - 2020-03-24

• added documentation
• 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)
  • 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
• 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: 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.

[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