Isotools

Latest version: v0.3.4

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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

* 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

* 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

* added documentation
* moved examples in documentation

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