Software Open Access

SLiMSuite v1.8.1 (2019-05-27)

Richard J. Edwards

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  "publisher": "Zenodo", 
  "DOI": "10.5281/zenodo.3229523", 
  "language": "eng", 
  "title": "SLiMSuite v1.8.1 (2019-05-27)", 
  "issued": {
    "date-parts": [
  "abstract": "<p>Please see the <a href=\"\">SLiMSuite GitHub repo</a> for updates to this code since release.</p>\n\n<p>This update has fast-forwarded the SLiMSuite release to <code>v1.8.1</code> to be consistent with the <code>tools/</code> wrapper script. A top level <code></code> file can now be run to access the main tools and functions of the package.</p>\n\n<p><a href=\"\">SLiMSuite REST servers</a> have been updated to match this release.</p>\n\n<p>A summary of the changes since the last release is given below.</p>\n\n<p>SLiMSuite updates</p>\n\n<p>Updates in Error/:</p>\n\n<p><strong>&bull; SLiMSuite:</strong> <em>Created/Renamed/moved.</em><br>\n&rarr; Version 1.4.0: SLiMSuite v1.4.0 (2018-07-02) release. Added this top level file to track overall version number.<br>\n&rarr; Version 1.4.1: SLiMBench v2.18.3 - Added better handling of motifs without TP occurrences for OccBench. Added minocctp=INT.</p>\n\n<p>Updates in extras/:</p>\n\n<p>&nbsp;</p>\n\n<p><strong>&bull; rje_pydocs:</strong> <em>Updated from Version 2.16.7.</em><br>\n&rarr; Version 2.16.8: Updated to to parse https.<br>\n&rarr; Version 2.16.9: Tweaked docstring parsing.</p>\n\n<p>Updates in libraries/:</p>\n\n<p><strong>&bull; rje:</strong> <em>Updated from Version 4.19.0.</em><br>\n&rarr; Version 4.19.1: Added code for catching non-ASCII log filenames.<br>\n&rarr; Version 4.20.0: Added quiet mode to log object and output of errors to stderr. Fixed rankList(unique=True)<br>\n&rarr; Version 4.21.0: Added hashlib MD% functions.<br>\n&rarr; Version 4.21.1: Fixed bug where silent=T wasn&#39;t running silent.</p>\n\n<p><strong>&bull; rje_blast_V2:</strong> <em>Updated from Version 2.22.2.</em><br>\n&rarr; Version 2.23.3: Fixed LocalIDCut error for GABLAM and QAssemble stat filtering.</p>\n\n<p><strong>&bull; rje_db:</strong> <em>Updated from Version 1.9.0.</em><br>\n&rarr; Version 1.9.1: Updated logging of adding/removing fields: default is now when debugging only.</p>\n\n<p><strong>&bull; rje_disorder:</strong> <em>Updated from Version 1.2.0.</em><br>\n&rarr; Version 1.3.0: Switched default behaviour to be md5acc=T.<br>\n&rarr; Version 1.4.0: Fixed up disorder=parse and disorder=foldindex.<br>\n&rarr; Version 1.5.0: Added iupred2 and anchor2 parsing from URL using accnum. Made default disorder=iushort2.</p>\n\n<p><strong>&bull; rje_genbank:</strong> <em>Updated from Version 1.5.3.</em><br>\n&rarr; Version 1.5.4: Added recognition of *.gbff for genbank files.</p>\n\n<p><strong>&bull; rje_obj:</strong> <em>Updated from Version 2.2.2.</em><br>\n&rarr; Version 2.3.0: Added quiet mode to object and stderr output.<br>\n&rarr; Version 2.4.0: Added vLog() and bugLog() methods.<br>\n&rarr; Version 2.4.1: Fixed bug where silent=T wasn&#39;t running silent.</p>\n\n<p><strong>&bull; rje_paf:</strong> <em>Created/Renamed/moved.</em><br>\n&rarr; Version 0.0.0: Initial Compilation.<br>\n&rarr; Version 0.1.0: Initial working version. Compatible with GABLAM v2.30.0 and Snapper v1.7.0.<br>\n&rarr; Version 0.2.0: Added endextend=X : Extend minimap2 hits to end of sequence if with X bp [10]<br>\n&rarr; Version 0.3.0: Added mapsplice mode for dealing with transcript mapping.<br>\n&rarr; Version 0.3.1: Correct PAF splicing bug.<br>\n&rarr; Version 0.4.0: Added TmpDir and forking for GABLAM conversion.<br>\n&rarr; Version 0.5.0: Added uniquehit=T/F : Option to use *.hitunique.tdt table of unique coverage for GABLAM coverage stats [False]</p>\n\n<p><strong>&bull; rje_ppi:</strong> <em>Updated from Version 2.8.1.</em><br>\n&rarr; Version 2.9.0: Added ppiout=FILE : Save pairwise PPI file following processing (if rest=None) [None]</p>\n\n<p><strong>&bull; rje_qsub:</strong> <em>Updated from Version 1.9.2.</em><br>\n&rarr; Version 1.9.3: Updates the order of the qsub -S /bin/bash flag.</p>\n\n<p><strong>&bull; rje_rmd:</strong> <em>Created/Renamed/moved.</em><br>\n&rarr; Version 0.0.0: Initial Compilation.</p>\n\n<p><strong>&bull; rje_samtools:</strong> <em>Updated from Version 1.20.0.</em><br>\n&rarr; Version 1.20.1: Fixed mlen bug. Added catching of unmapped reads in SAM file. Fixed RLen bug. Changed softclip defaults.<br>\n&rarr; Version 1.20.2: Fixed readlen coverage bug and acut bug.</p>\n\n<p><strong>&bull; rje_seq:</strong> <em>Updated from Version 3.25.0.</em><br>\n&rarr; Version 3.25.1: Fixed -long_seqids retrieval bug.<br>\n&rarr; Version 3.25.2: Fixed 9spec filtering bug.</p>\n\n<p><strong>&bull; rje_seqlist:</strong> <em>Updated from Version 1.29.0.</em><br>\n&rarr; Version 1.30.0: Updated and improved DNA2Protein.<br>\n&rarr; Version 1.31.0: Added genecounter to rename option for use with other programs, e.g. PAGSAT.<br>\n&rarr; Version 1.31.1: Fixed edit bug when not in DNA mode.<br>\n&rarr; Version 1.32.0: Added genomesize and NG50/LG50 to DNA summarise.<br>\n&rarr; Version 1.32.1: Fixed LG50/L50 bug.</p>\n\n<p><strong>&bull; rje_sequence:</strong> <em>Updated from Version 2.6.0.</em><br>\n&rarr; Version 2.7.0: Added shift=X to maskRegion() for 1-L input. Fixed cterminal maskRegion.</p>\n\n<p><strong>&bull; rje_slimcore:</strong> <em>Updated from Version 2.9.0.</em><br>\n&rarr; Version 2.10.0: Added seqfilter=T/F : Whether to apply sequence filtering options (goodX, badX etc.) to input [False]<br>\n&rarr; Version 2.10.1: Fixed default results file bug.<br>\n&rarr; Version 2.10.2: Improved handling and REST output of disorder scores.<br>\n&rarr; Version 2.11.0: Modified qregion=X,Y to be 1-L numbering.</p>\n\n<p><strong>&bull; rje_slimlist:</strong> <em>Updated from Version 1.7.3.</em><br>\n&rarr; Version 1.7.4: Modified concetanation of SLiMSuite results to use &quot;|&quot; in place of &quot;#&quot; for better compatibility.</p>\n\n<p><strong>&bull; rje_uniprot:</strong> <em>Updated from Version 3.25.0.</em><br>\n&rarr; Version 3.25.1: Fixed proteome download bug following Uniprot changes.<br>\n&rarr; Version 3.25.2: Fixed Uniprot protein extraction issues by using curl. (May not be a robust fix!)</p>\n\n<p>Updates in tools/:</p>\n\n<p>&nbsp;</p>\n\n<p><strong>&bull; buscomp:</strong> <em>Created/Renamed/moved.</em><br>\n&rarr; Version 0.0.0: Initial Compilation.<br>\n&rarr; Version 0.1.0: Basic working version.<br>\n&rarr; Version 0.2.0: Functional version with basic RMarkdown HTML output.<br>\n&rarr; Version 0.3.0: Added ratefas=FILELIST: Additional fasta files of assemblies to rate with BUSCOMPSeq (No BUSCO run) [].<br>\n&rarr; Version 0.4.0: Implemented forking and tidied up output a little.<br>\n&rarr; Version 0.5.0: Updated genome stats and RMarkdown HTML output. Reorganised assembly loading and proeccessing. Added menus.<br>\n&rarr; Version 0.5.1: Reorganised code for clearer flow and documentation. Unique and missing BUSCO output added.<br>\n&rarr; Version 0.5.2: Dropped paircomp method and added Rmarkdown control methods. Updated Rmarkdown descriptions. Updated log output.<br>\n&rarr; Version 0.5.3: Tweaked log output and fixed a few minor bugs.<br>\n&rarr; Version 0.5.4: Deleted some excess code and tweaked BUSCO percentage plot outputs.<br>\n&rarr; Version 0.5.5: Fixed minlocid bug and cleared up minimap temp directories. Added LnnIDxx to BUSCOMP outputs.<br>\n&rarr; Version 0.5.6: Added uniquehit=T/F : Option to use *.hitunique.tdt table of unique coverage for GABLAM coverage stats [False]<br>\n&rarr; Version 0.6.0: Added more minimap options, changed defaults and dev generation of a table changes in ratings from BUSCO to BUSCOMP.<br>\n&rarr; Version 0.6.1: Fixed bug that was including Duplicated sequences in the buscomp.fasta file. Added option to exclude from BUSCOMPSeq compilation.<br>\n&rarr; Version 0.6.2: Fixed bug introduced that had broken manual group review/editing.<br>\n&rarr; Version 0.7.0: Updated the defaults in the light of test analyses. Tweaked Rmd report.<br>\n&rarr; Version 0.7.1: Fixed unique group count bug when some genomes are not in a group. Fixed running with non-standard options.<br>\n&rarr; Version 0.7.2: Added loadsummary=T/F option to regenerate summaries and fixed bugs running without BUSCO results.</p>\n\n<p><strong>&bull; comparimotif_V3:</strong> <em>Updated from Version 3.13.0.</em><br>\n&rarr; Version 3.14.0: Modified memsaver mode to take different input formats.</p>\n\n<p><strong>&bull; gablam:</strong> <em>Updated from Version 2.29.0.</em><br>\n&rarr; Version 2.30.0: Added mapper=X : Program to use for mapping files against each other (blast/minimap) [blast]<br>\n&rarr; Version 2.30.1: Fixed BLAST LocalIDCut error for GABLAM and QAssemble stat filtering.</p>\n\n<p><strong>&bull; gopher:</strong> <em>Updated from Version 3.4.3.</em><br>\n&rarr; Version 3.5.0: Added separate outputs for trees with different alignment programs.<br>\n&rarr; Version 3.5.1: Added capacity to run DNA GOPHER with tblastx. (Not tested!)<br>\n&rarr; 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.</p>\n\n<p><strong>&bull; haqesac:</strong> <em>Updated from Version 1.12.0.</em><br>\n&rarr; Version 1.13.0: Modified qregion=X,Y to be 1-L numbering.</p>\n\n<p><strong>&bull; pagsat:</strong> <em>Updated from Version 2.4.0.</em><br>\n&rarr; Version 2.5.0: Reduced the executed code when mapfas=T assessment=F. (Recommended first run.) Added renaming.<br>\n&rarr; Version 2.5.1: Added recognition of *.gbff for genbank files.<br>\n&rarr; Version 2.6.0: Added mapper=X : Program to use for mapping files against each other (blast/minimap) [blast]<br>\n&rarr; Version 2.6.1: Switch failure to find key report files to a long warning, not program exit.<br>\n&rarr; Version 2.6.2: Fixed bugs with mapper=minimap mode and started adding more internal documentation.<br>\n&rarr; Version 2.6.3: Fixed default behaviour to run report=T mode.<br>\n&rarr; Version 2.6.4: Fixed summary table merge bug.<br>\n&rarr; Version 2.6.5: Fixed compile path bug.<br>\n&rarr; Version 2.6.6: Fixed BLAST LocalIDCut error for GABLAM and QAssemble stat filtering.<br>\n&rarr; Version 2.6.7: Generalised compile path bug fix.<br>\n&rarr; Version 2.6.8: Added ChromXcov fields to PAGSAT Compare.</p>\n\n<p><strong>&bull; pingu_V4:</strong> <em>Updated from Version 4.9.0.</em><br>\n&rarr; Version 4.9.1: Fixed Pairwise parsing and filtering for more flexibility of input. Fixed fasid=X bug and ppiseqfile names.<br>\n&rarr; Version 4.10.0: Added hubfield and spokefield options for parsing hublist.</p>\n\n<p><strong>&bull; qslimfinder:</strong> <em>Updated from Version 2.2.0.</em><br>\n&rarr; Version 2.3.0: Modified qregion=X,Y to be 1-L numbering.</p>\n\n<p><strong>&bull; samphaser:</strong> <em>Created/Renamed/moved.</em><br>\n&rarr; Version 0.0.0: Initial Compilation.<br>\n&rarr; Version 0.1.0: Updated SAMPhaser to be more memory efficient.<br>\n&rarr; Version 0.2.0: Added reading of sequence and generation of SNP-altered haplotype blocks.<br>\n&rarr; Version 0.2.1: Fixed bug in which zero-phasing sequences were being excluded from blocks output.<br>\n&rarr; Version 0.3.0: Made a new unzip process.<br>\n&rarr; Version 0.4.0: Added RGraphics for unzip.<br>\n&rarr; Version 0.4.1: Fixed MeanX bug in devUnzip.<br>\n&rarr; Version 0.4.2: Made phaseindels=F by default: mononucleotide indel errors will probably add phasing noise. Fixed basefile R bug.<br>\n&rarr; Version 0.4.3: Fixed bug introduced by adding depthplot code. Fixed phaseindels bug. (Wasn&#39;t working!)<br>\n&rarr; Version 0.4.4: Modified mincut=X to adjust for samtools V1.12.0.<br>\n&rarr; Version 0.4.5: Updated for modified RJE_SAMTools output.<br>\n&rarr; Version 0.4.6: splitzero=X : Whether to split haplotigs at zero-coverage regions of X+ bp (-1 = no split) [100]<br>\n&rarr; Version 0.5.0: snptable=T/F : Output filtered alleles to SNP Table [False]<br>\n&rarr; Version 0.6.0: Converted haplotig naming to be consistent for PAGSAT generation. Updated for rje_samtools v1.21.1.<br>\n&rarr; Version 0.7.0: Added skiploci=LIST and phaseloci=LIST : Optional list of loci to skip phasing []<br>\n&rarr; Version 0.8.0: poordepth=T/F : Whether to include reads with poor track probability in haplotig depth plots (random track) [False]</p>\n\n<p><strong>&bull; seqmapper:</strong> <em>Updated from Version 2.2.0.</em><br>\n&rarr; Version 2.3.0: Added GABLAM-free method.</p>\n\n<p><strong>&bull; seqsuite:</strong> <em>Updated from Version 1.19.1.</em><br>\n&rarr; Version 1.20.0: Added rje_paf.PAF.<br>\n&rarr; Version 1.21.0: Added NG50 and LG50 to batch summarise.<br>\n&rarr; Version 1.22.0: Added BUSCOMP to programs.<br>\n&rarr; Version 1.23.0: Added rje_ppi.PPI to programs.</p>\n\n<p><strong>&bull; slimbench:</strong> <em>Updated from Version 2.18.2.</em><br>\n&rarr; Version 2.18.3: Added better handling of motifs without TP occurrences for OccBench. Added minocctp=INT.<br>\n&rarr; Version 2.18.4: Fixed ELMBench rating bug.<br>\n&rarr; Version 2.18.5: Fixed Balanced=F bug.<br>\n&rarr; Version 2.19.0: Implemented dataset=LIST: List of headers to split dataset into. If blank, will use datatype defaults. []</p>\n\n<p><strong>&bull; slimfarmer:</strong> <em>Updated from Version 1.9.0.</em><br>\n&rarr; Version 1.10.0: Added appending contents of jobini file to slimsuite=F farm commands.</p>\n\n<p><strong>&bull; slimfinder:</strong> <em>Updated from Version 5.3.4.</em><br>\n&rarr; Version 5.3.5: Fixed slimcheck and advanced stats models bug.<br>\n&rarr; Version 5.4.0: Modified qregion=X,Y to be 1-L numbering.</p>\n\n<p><strong>&bull; slimparser:</strong> <em>Updated from Version 0.5.0.</em><br>\n&rarr; Version 0.5.1: Minor docs and bug fixes.<br>\n&rarr; Version 0.6.0: Improved functionality as replacement pureapi with rest=jobid and rest=check functions.</p>\n\n<p><strong>&bull; slimsuite:</strong> <em>Updated from Version 1.7.1.</em><br>\n&rarr; Version 1.8.0: Added BUSCOMP and basic test function.<br>\n&rarr; Version 1.8.1: Updated documentation and added IUPred2. General tidy up and new example data for protocols paper.</p>\n\n<p><strong>&bull; smrtscape:</strong> <em>Updated from Version 2.2.2.</em><br>\n&rarr; Version 2.2.3: Fixed bug where SMRT subreads are not returned by seqlist in correct order. Fixed RQ=0 bug.</p>\n\n<p><strong>&bull; snapper:</strong> <em>Updated from Version 1.6.1.</em><br>\n&rarr; Version 1.7.0: Added mapper=minimap setting, compatible with GABLAM v2.30.0 and rje_paf v0.1.0.</p>\n\n<p>&copy; RJ Edwards 2019. Last modified 27 May 2019.</p>\n\n<p>&nbsp;</p>", 
  "author": [
      "family": "Richard J. Edwards"
  "version": "v1.8.1", 
  "type": "article", 
  "id": "3229523"
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