Software Open Access

SLiMSuite v1.8.1 (2019-05-27)

Richard J. Edwards


JSON Export

{
  "files": [
    {
      "links": {
        "self": "https://zenodo.org/api/files/b0baf4f1-2df7-41c4-bf86-3d3a1734d35b/slimsuite/SLiMSuite-v1.8.1.zip"
      }, 
      "checksum": "md5:9fecfc345f8e0ed6168379407c069f5a", 
      "bucket": "b0baf4f1-2df7-41c4-bf86-3d3a1734d35b", 
      "key": "slimsuite/SLiMSuite-v1.8.1.zip", 
      "type": "zip", 
      "size": 18693832
    }
  ], 
  "owners": [
    14754
  ], 
  "doi": "10.5281/zenodo.3229523", 
  "stats": {
    "version_unique_downloads": 26.0, 
    "unique_views": 85.0, 
    "views": 95.0, 
    "version_views": 298.0, 
    "unique_downloads": 24.0, 
    "version_unique_views": 246.0, 
    "volume": 486039632.0, 
    "version_downloads": 35.0, 
    "downloads": 26.0, 
    "version_volume": 639926357.0
  }, 
  "links": {
    "doi": "https://doi.org/10.5281/zenodo.3229523", 
    "conceptdoi": "https://doi.org/10.5281/zenodo.593828", 
    "bucket": "https://zenodo.org/api/files/b0baf4f1-2df7-41c4-bf86-3d3a1734d35b", 
    "conceptbadge": "https://zenodo.org/badge/doi/10.5281/zenodo.593828.svg", 
    "html": "https://zenodo.org/record/3229523", 
    "latest_html": "https://zenodo.org/record/3229523", 
    "badge": "https://zenodo.org/badge/doi/10.5281/zenodo.3229523.svg", 
    "latest": "https://zenodo.org/api/records/3229523"
  }, 
  "conceptdoi": "10.5281/zenodo.593828", 
  "created": "2019-05-27T03:50:14.252748+00:00", 
  "updated": "2020-01-25T19:22:36.380705+00:00", 
  "conceptrecid": "593828", 
  "revision": 7, 
  "id": 3229523, 
  "metadata": {
    "access_right_category": "success", 
    "doi": "10.5281/zenodo.3229523", 
    "description": "<p>Please see the <a href=\"https://github.com/slimsuite/SLiMSuite\">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/slimsuite.py</code> wrapper script. A top level <code>SLiMSuite.py</code> file can now be run to access the main tools and functions of the package.</p>\n\n<p><a href=\"http://rest.slimsuite.unsw.edu.au\">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>", 
    "language": "eng", 
    "title": "SLiMSuite v1.8.1 (2019-05-27)", 
    "license": {
      "id": "GPL-3.0+"
    }, 
    "relations": {
      "version": [
        {
          "count": 5, 
          "index": 4, 
          "parent": {
            "pid_type": "recid", 
            "pid_value": "593828"
          }, 
          "is_last": true, 
          "last_child": {
            "pid_type": "recid", 
            "pid_value": "3229523"
          }
        }
      ]
    }, 
    "version": "v1.8.1", 
    "keywords": [
      "slimsuite", 
      "bioinformatics", 
      "motif discovery", 
      "sequence analysis"
    ], 
    "publication_date": "2019-05-27", 
    "creators": [
      {
        "orcid": "0000-0002-3645-5539", 
        "affiliation": "University of New South Wales", 
        "name": "Richard J. Edwards"
      }
    ], 
    "access_right": "open", 
    "resource_type": {
      "type": "software", 
      "title": "Software"
    }, 
    "related_identifiers": [
      {
        "scheme": "url", 
        "identifier": "https://github.com/slimsuite/SLiMSuite/tree/v1.8.1", 
        "relation": "isSupplementTo"
      }, 
      {
        "scheme": "doi", 
        "identifier": "10.5281/zenodo.593828", 
        "relation": "isVersionOf"
      }
    ]
  }
}
298
35
views
downloads
All versions This version
Views 29895
Downloads 3526
Data volume 639.9 MB486.0 MB
Unique views 24685
Unique downloads 2624

Share

Cite as