Please see the SLiMSuite GitHub repo for updates to this code since release. This update has fast-forwarded the SLiMSuite release to v1.8.1 to be consistent with the tools/slimsuite.py wrapper script. A top level SLiMSuite.py file can now be run to access the main tools and functions of the package. SLiMSuite REST servers have been updated to match this release. A summary of the changes since the last release is given below. SLiMSuite updates Updates in Error/: • SLiMSuite: Created/Renamed/moved. → Version 1.4.0: SLiMSuite v1.4.0 (2018-07-02) release. Added this top level file to track overall version number. → Version 1.4.1: SLiMBench v2.18.3 - Added better handling of motifs without TP occurrences for OccBench. Added minocctp=INT. Updates in extras/: • rje_pydocs: Updated from Version 2.16.7. → Version 2.16.8: Updated to to parse https. → Version 2.16.9: Tweaked docstring parsing. Updates in libraries/: • rje: Updated from Version 4.19.0. → Version 4.19.1: Added code for catching non-ASCII log filenames. → Version 4.20.0: Added quiet mode to log object and output of errors to stderr. Fixed rankList(unique=True) → Version 4.21.0: Added hashlib MD% functions. → Version 4.21.1: Fixed bug where silent=T wasn't running silent. • rje_blast_V2: Updated from Version 2.22.2. → Version 2.23.3: Fixed LocalIDCut error for GABLAM and QAssemble stat filtering. • rje_db: Updated from Version 1.9.0. → Version 1.9.1: Updated logging of adding/removing fields: default is now when debugging only. • rje_disorder: Updated from Version 1.2.0. → Version 1.3.0: Switched default behaviour to be md5acc=T. → Version 1.4.0: Fixed up disorder=parse and disorder=foldindex. → Version 1.5.0: Added iupred2 and anchor2 parsing from URL using accnum. Made default disorder=iushort2. • rje_genbank: Updated from Version 1.5.3. → Version 1.5.4: Added recognition of *.gbff for genbank files. • rje_obj: Updated from Version 2.2.2. → Version 2.3.0: Added quiet mode to object and stderr output. → Version 2.4.0: Added vLog() and bugLog() methods. → Version 2.4.1: Fixed bug where silent=T wasn't running silent. • rje_paf: Created/Renamed/moved. → Version 0.0.0: Initial Compilation. → Version 0.1.0: Initial working version. Compatible with GABLAM v2.30.0 and Snapper v1.7.0. → Version 0.2.0: Added endextend=X : Extend minimap2 hits to end of sequence if with X bp [10] → Version 0.3.0: Added mapsplice mode for dealing with transcript mapping. → Version 0.3.1: Correct PAF splicing bug. → Version 0.4.0: Added TmpDir and forking for GABLAM conversion. → Version 0.5.0: Added uniquehit=T/F : Option to use *.hitunique.tdt table of unique coverage for GABLAM coverage stats [False] • rje_ppi: Updated from Version 2.8.1. → Version 2.9.0: Added ppiout=FILE : Save pairwise PPI file following processing (if rest=None) [None] • rje_qsub: Updated from Version 1.9.2. → Version 1.9.3: Updates the order of the qsub -S /bin/bash flag. • rje_rmd: Created/Renamed/moved. → Version 0.0.0: Initial Compilation. • rje_samtools: Updated from Version 1.20.0. → Version 1.20.1: Fixed mlen bug. Added catching of unmapped reads in SAM file. Fixed RLen bug. Changed softclip defaults. → Version 1.20.2: Fixed readlen coverage bug and acut bug. • rje_seq: Updated from Version 3.25.0. → Version 3.25.1: Fixed -long_seqids retrieval bug. → Version 3.25.2: Fixed 9spec filtering bug. • rje_seqlist: Updated from Version 1.29.0. → Version 1.30.0: Updated and improved DNA2Protein. → Version 1.31.0: Added genecounter to rename option for use with other programs, e.g. PAGSAT. → Version 1.31.1: Fixed edit bug when not in DNA mode. → Version 1.32.0: Added genomesize and NG50/LG50 to DNA summarise. → Version 1.32.1: Fixed LG50/L50 bug. • rje_sequence: Updated from Version 2.6.0. → Version 2.7.0: Added shift=X to maskRegion() for 1-L input. Fixed cterminal maskRegion. • rje_slimcore: Updated from Version 2.9.0. → Version 2.10.0: Added seqfilter=T/F : Whether to apply sequence filtering options (goodX, badX etc.) to input [False] → Version 2.10.1: Fixed default results file bug. → Version 2.10.2: Improved handling and REST output of disorder scores. → Version 2.11.0: Modified qregion=X,Y to be 1-L numbering. • rje_slimlist: Updated from Version 1.7.3. → Version 1.7.4: Modified concetanation of SLiMSuite results to use "|" in place of "#" for better compatibility. • rje_uniprot: Updated from Version 3.25.0. → Version 3.25.1: Fixed proteome download bug following Uniprot changes. → Version 3.25.2: Fixed Uniprot protein extraction issues by using curl. (May not be a robust fix!) Updates in tools/: • buscomp: Created/Renamed/moved. → Version 0.0.0: Initial Compilation. → Version 0.1.0: Basic working version. → Version 0.2.0: Functional version with basic RMarkdown HTML output. → Version 0.3.0: Added ratefas=FILELIST: Additional fasta files of assemblies to rate with BUSCOMPSeq (No BUSCO run) []. → Version 0.4.0: Implemented forking and tidied up output a little. → Version 0.5.0: Updated genome stats and RMarkdown HTML output. Reorganised assembly loading and proeccessing. Added menus. → Version 0.5.1: Reorganised code for clearer flow and documentation. Unique and missing BUSCO output added. → Version 0.5.2: Dropped paircomp method and added Rmarkdown control methods. Updated Rmarkdown descriptions. Updated log output. → Version 0.5.3: Tweaked log output and fixed a few minor bugs. → Version 0.5.4: Deleted some excess code and tweaked BUSCO percentage plot outputs. → Version 0.5.5: Fixed minlocid bug and cleared up minimap temp directories. Added LnnIDxx to BUSCOMP outputs. → Version 0.5.6: Added uniquehit=T/F : Option to use *.hitunique.tdt table of unique coverage for GABLAM coverage stats [False] → Version 0.6.0: Added more minimap options, changed defaults and dev generation of a table changes in ratings from BUSCO to BUSCOMP. → Version 0.6.1: Fixed bug that was including Duplicated sequences in the buscomp.fasta file. Added option to exclude from BUSCOMPSeq compilation. → Version 0.6.2: Fixed bug introduced that had broken manual group review/editing. → Version 0.7.0: Updated the defaults in the light of test analyses. Tweaked Rmd report. → Version 0.7.1: Fixed unique group count bug when some genomes are not in a group. Fixed running with non-standard options. → Version 0.7.2: Added loadsummary=T/F option to regenerate summaries and fixed bugs running without BUSCO results. • comparimotif_V3: Updated from Version 3.13.0. → Version 3.14.0: Modified memsaver mode to take different input formats. • gablam: Updated from Version 2.29.0. → Version 2.30.0: Added mapper=X : Program to use for mapping files against each other (blast/minimap) [blast] → Version 2.30.1: Fixed BLAST LocalIDCut error for GABLAM and QAssemble stat filtering. • gopher: Updated from Version 3.4.3. → Version 3.5.0: Added separate outputs for trees with different alignment programs. → Version 3.5.1: Added capacity to run DNA GOPHER with tblastx. (Not tested!) → Version 3.5.2: Added acc=LIST as alias for uniprotid=LIST and updated docstring for REST to make it clear that rest=X needed. • haqesac: Updated from Version 1.12.0. → Version 1.13.0: Modified qregion=X,Y to be 1-L numbering. • pagsat: Updated from Version 2.4.0. → Version 2.5.0: Reduced the executed code when mapfas=T assessment=F. (Recommended first run.) Added renaming. → Version 2.5.1: Added recognition of *.gbff for genbank files. → Version 2.6.0: Added mapper=X : Program to use for mapping files against each other (blast/minimap) [blast] → Version 2.6.1: Switch failure to find key report files to a long warning, not program exit. → Version 2.6.2: Fixed bugs with mapper=minimap mode and started adding more internal documentation. → Version 2.6.3: Fixed default behaviour to run report=T mode. → Version 2.6.4: Fixed summary table merge bug. → Version 2.6.5: Fixed compile path bug. → Version 2.6.6: Fixed BLAST LocalIDCut error for GABLAM and QAssemble stat filtering. → Version 2.6.7: Generalised compile path bug fix. → Version 2.6.8: Added ChromXcov fields to PAGSAT Compare. • pingu_V4: Updated from Version 4.9.0. → Version 4.9.1: Fixed Pairwise parsing and filtering for more flexibility of input. Fixed fasid=X bug and ppiseqfile names. → Version 4.10.0: Added hubfield and spokefield options for parsing hublist. • qslimfinder: Updated from Version 2.2.0. → Version 2.3.0: Modified qregion=X,Y to be 1-L numbering. • samphaser: Created/Renamed/moved. → Version 0.0.0: Initial Compilation. → Version 0.1.0: Updated SAMPhaser to be more memory efficient. → Version 0.2.0: Added reading of sequence and generation of SNP-altered haplotype blocks. → Version 0.2.1: Fixed bug in which zero-phasing sequences were being excluded from blocks output. → Version 0.3.0: Made a new unzip process. → Version 0.4.0: Added RGraphics for unzip. → Version 0.4.1: Fixed MeanX bug in devUnzip. → Version 0.4.2: Made phaseindels=F by default: mononucleotide indel errors will probably add phasing noise. Fixed basefile R bug. → Version 0.4.3: Fixed bug introduced by adding depthplot code. Fixed phaseindels bug. (Wasn't working!) → Version 0.4.4: Modified mincut=X to adjust for samtools V1.12.0. → Version 0.4.5: Updated for modified RJE_SAMTools output. → Version 0.4.6: splitzero=X : Whether to split haplotigs at zero-coverage regions of X+ bp (-1 = no split) [100] → Version 0.5.0: snptable=T/F : Output filtered alleles to SNP Table [False] → Version 0.6.0: Converted haplotig naming to be consistent for PAGSAT generation. Updated for rje_samtools v1.21.1. → Version 0.7.0: Added skiploci=LIST and phaseloci=LIST : Optional list of loci to skip phasing [] → Version 0.8.0: poordepth=T/F : Whether to include reads with poor track probability in haplotig depth plots (random track) [False] • seqmapper: Updated from Version 2.2.0. → Version 2.3.0: Added GABLAM-free method. • seqsuite: Updated from Version 1.19.1. → Version 1.20.0: Added rje_paf.PAF. → Version 1.21.0: Added NG50 and LG50 to batch summarise. → Version 1.22.0: Added BUSCOMP to programs. → Version 1.23.0: Added rje_ppi.PPI to programs. • slimbench: Updated from Version 2.18.2. → Version 2.18.3: Added better handling of motifs without TP occurrences for OccBench. Added minocctp=INT. → Version 2.18.4: Fixed ELMBench rating bug. → Version 2.18.5: Fixed Balanced=F bug. → Version 2.19.0: Implemented dataset=LIST: List of headers to split dataset into. If blank, will use datatype defaults. [] • slimfarmer: Updated from Version 1.9.0. → Version 1.10.0: Added appending contents of jobini file to slimsuite=F farm commands. • slimfinder: Updated from Version 5.3.4. → Version 5.3.5: Fixed slimcheck and advanced stats models bug. → Version 5.4.0: Modified qregion=X,Y to be 1-L numbering. • slimparser: Updated from Version 0.5.0. → Version 0.5.1: Minor docs and bug fixes. → Version 0.6.0: Improved functionality as replacement pureapi with rest=jobid and rest=check functions. • slimsuite: Updated from Version 1.7.1. → Version 1.8.0: Added BUSCOMP and basic test function. → Version 1.8.1: Updated documentation and added IUPred2. General tidy up and new example data for protocols paper. • smrtscape: Updated from Version 2.2.2. → Version 2.2.3: Fixed bug where SMRT subreads are not returned by seqlist in correct order. Fixed RQ=0 bug. • snapper: Updated from Version 1.6.1. → Version 1.7.0: Added mapper=minimap setting, compatible with GABLAM v2.30.0 and rje_paf v0.1.0. © RJ Edwards 2019. Last modified 27 May 2019.