Release 1.4.2

• Fixed splitFasta that NovelORF peptides coding transcripts not recognized correctly.

Release 1.4.1

[1.4.1] - 2024-05-26

• Fixed VariantPepidePool that old versions of SeqUtils.molecular_weight don't handle SeqRecord objects. #874

Release 1.4.0

[1.4.0] - 2024-03-27

• --coding-novel-orf added to callNoncoding and callVariant to call novel ORF peptides from coding transcripts. #659

• Renamed callNoncoding to callNovelORF and replaced the internal source type Noncoding to NovelORF. #863

Release 1.3.1

[1.3.1] - 2024-03-18

Added:

• Flag --backsplicing-only added to callVariant to allow only calling noncanonical peptides spanning backsplicing site from circRNA events. #858

Release 1.3.0

Fixed:

• Adjacent variants were not merged as MNVs successfully. The function always exited with nothing.

• Because of the updating to on-disk GTF, the coding transcripts were not generated and saved successfully. filterFasta is the only command affected.

• Updated splitFasta and summarizeFasta to accept source combinations in --order-source.

• Fixed parseCIRCexplorer so the exon/intron indices in variant IDs are sorted correctly.

• Fixed parseVEP to handle insertions in start-inclusion. #840

• Fixed callVariant of 'no reference out node found'. #842

• Fixed mergeFasta to remove redundant FASTA header entries. #846

• Fixed GenomicAnnotation to parse ENSEMBL style UTR correctly. #687

• Switch to use python's logging package for logging.

• Print basic summary to callVariant output. #412

Add

• Added --timeout-seconds to callVariant.

• Added metadata.json to the index directory for all essential parameters of how a moPepGen index directory is created, including cleavage parameters. #850

• Added updateIndex #853

• Output a peptide table for additional information. #833

Release 1.2.1

Add

• Added --graph-output-dir to save graph data in json.

Fixed

• Fixed summarizeFasta that SEC and W2F on fusion peptides are ignored. #789

• Fixed callVariant that variant_coordinates_to_gene failed when the deletion is end inclusion and it overlaps with the last nucleotide of an exon. #793

• Fixed splitFasta that CodonReassign and SECT were not able to be grouped. #796

• Fixed callVariant that in-frame subgraphs not recognized when they are not in variant bubble.

• Fixed callVariant that peptides are falsely called if the last miscleaved node is missing a downstream cleavage altering variant. #800

• Fixed TVGNode that get_max_subgraph_id always returns the last subgraph ID. #802

• Fixed callVariant with altSplice insertion with intronic frameshift variant which is very closed to the end of the subgraph. #803

• Fixed bruteForce that accepter variants are skipped if the donor transcript has variants with the same coordinate. #810

• Fixed splitFasta that source and source group order gets overriden by GVF order. #805

• Fixed summarizeFasta and splitFasta being too slow. #795

• Fixed splitFasta to use top priority header for additional split

• Fixed callVariant that some accepter only ORFs maybe included for noncoding fusion transcripts.

• Fixed callVariant that when filtering variants for a given transcript/fusion/circRNA, coordinates of end inclusion insertions were not interpreted correctly.

• Fixed bruteForce that selenocysteine not fixed for deletion alt sequence.

• Fixed callVariant that nodes with fusion being treated as subgraph out or end node incorrectly.

• Fixed callVariant that upstream cleavage altering variants were affecting checks for whether a node is hybrid in circRNA.

• Fixed callVariant that two SNV at the same location in circRNA was affecting hybrid node identification.

• Fixed callVariant. When creating the cleavage graph, when a variant bubble is processed, the downstream node(s) needs to be identified for the next iteration, and only in-frame node should be used. However some nodes can span over two reading frames, so we should check the last reading frame index instead of the first.

• Fixed callVariant that accepter transcript variants very closed to the breakpoint were skipped.

Added

• Added support for --group-source for summarizeFasta. #798

Release 1.2.0

Fixed

• Fixed that reference source are not recognized. Switched to use upper case values. #758

• Fixed generateIndex that symlink was not created properly for GTF with --gtf-symlink.

• Fixed matplotlib warning message #742

• Fixed parseVEP that insertions not parsed successfully if the location is a single base. #766

• Fixed callVariant that peptides with upstream cleavage altering mutations were not called. #670

• Fixed fuzzTest to take multiple CPUs and use temporary directory.

• Fixed issue in callVariant of circRNA with a SNV being silent in the first loop but not in the second.

• Fixed issue that circRNA peptide nodes with and without a silent mutation were collapsed. #778

• Fixed that circRNA peptides that carry indels incompatible with the orf start node should not be called. #780

• Fixed that hybrid node was not identified if the variant is in the end of an exon. #782

• Fixed that in circRNA, cleavage gain from upstream node is added to the the wrong ORF. #783

• Fixed callVariant that fit_into_codon terminated early in fusion transcripts when there donor has a frameshift and accepter has a variant right after the breakpoint. #786

Release 1.1.0

Fixed

• Reduced memory usage by mapping the GTF files into memory instead of reading it all at once. #371

Release 1.0.0

Added

• Added the support for calling peptides of Selenocysteine terminated. #684

• Added the support for calling peptides of W > F codon reassignments. #484

• Added the support for calling peptides with adjacent SNP/INDEL. #691

• Updated fake.py and bruteForce to handle selenocysteine, W2F and MNV. #689

• callAltTranslation added to call peptides with alternative translation without any genomic or transcriptomic variations.

• Enabled summarizeFasta to create bar plot of the summary results.

Fixed

• Fixed fake that simulated selenocysteine positions could be in introns.

• Fixed fake that the last exon was picked for A3SS or first exon for A5SS.

• Fixed fusion with very small intronic insertion. #707

• In ThreeFrameTVG when aligning variant bubbles and when nodes are merged, variants were not merged correctly.

• Fixed TVG that indel merged with downstream fusion treated as subgraph out. #708

• Fixed parseRMATS to handle more complex situations such as exons interjacent between splicing sites and exons spanning over the splicing site. #715, #716, #717, and PR #720

• Fixed callVariant that failed when there is a SNV very close to the end on a AltSplice insertion. #723

• Fixed TranscriptAnnotationModel for not recognizing transcripts with mRNA_end_NF correctly. #724

• Fixed callVariant issue of altSplice insertion carries an intronic indel that goes back to the original reading frame. #726

• Fixed callVariant to handle deletion that spans over an entire intron. #732

• Fixed callVariant to skip peptides earlier if they are either too long or too short to significantly improve efficiency. #736

• Fixed callVariant to handle hypermutated region with a dynamic cutoff. #738

• Fixed decoyFasta to make it as default to keep cleavage site amino acid residues unmodified. #750

• Fixed SeqFeature and GTFSeqFeature to remove the definition of strand and use location.strand. #616

• Refactored util so all functions are accessible. #749

Release 0.11.3

Fixed

• filterFasta failed with the new noncoding peptide FASTA header. #675