Version 0.3.4

[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.

Version 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 highlighing, code style, additional explanations on filtering

Version 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.

Version 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

Version 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 accross intron chains
• changed default parameter of filter_query in run_isotools script to "FSM or not (INTERNAL_PRIMING or RTTS)"

Version 0.2.11.1

[0.2.11.1]

• bugfix: KeyError during transcriptome reconstruction in _add_chimeric.
• bugfix: default colors in plot_diff_results.

Version 0.2.11

• added function to import samples from csv/gtf to import transcriptome reconstructions / quantifications from other tools.
• dropped requirement for gtf files to be tabix indexed.

Version 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.

Version 0.2.9

Changes

• 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

Version 0.2.8

• fix: version information lost when pickeling reference.
• fix missing genen 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