SLiMSuite Servers out of action

Following a move out of academia and lack of ongoing funding, the SLiMSuite website and servers at UNSW are currently out of action. It is not clear at this point whether they will be restored, replaced, or permanently retired. SLiMSuite programs and code are still available from GitHub. Please get in touch if you have any questions during this transition period.

SLiMSuite release v1.11.0 (2022-01-12)

SLiMSuite v1.11 sees the introduction of six genome assembly tools:

• DepthCharge = Genome assembly quality control and misassembly repair. DepthCharge is an assembly quality control and misassembly repair program. It uses mapped long read depth of coverage to charge through a genome assembly and identify coverage “cliffs” that may indicate a misassembly. If appropriate, it will then blast the assembly into fragment at those misassemblies.
• DepthKopy = DepthKopy: Read-depth based copy number estimation. DepthKopy applies the same single-copy read depth estimate as DepthSizer to estimate the copy number of different gene regions in a slightly modified version of the approach used in the basenji genome paper.
• DepthSizer = DepthSizer: Read-depth based genome size prediction. DepthSizer uses long-read depth profiles and BUSCO single-copy orthologues to predict genome size. DepthSizer works on the principle that Complete BUSCO genes should represent predominantly single copy (diploid read depth) regions along with some poor quality and/or repeat regions. Assembly artefacts and collapsed repeats etc. are predicted to deviate from diploid read depth in an inconsistent manner. Therefore, even if less than half the region is actually diploid coverage, the modal read depth is expected to represent the actual single copy read depth.
• GapSpanner = GapSpanner: Genome assembly gap long read support and reassembly tool. GapSpanner uses (or generates) a BAM file of long reads mapped to a genome assembly to assess assembly “gaps” for spanning read support. Optionally, reads spanning each gap can be extracted and re-assembled with Flye. If the new assembly spans the gap, crude gap-filling can be performed. This will be reversed if edits are not subsequently supported by spanning reads mapped onto the updated assembly.
• NUMTFinder = NUMTFinder: Nuclear mitochondrial fragment (NUMT) search tool. NUMTFinder uses a mitochondrial genome to search against genome assembly and identify putative NUMTs. NUMT fragments are then combined into NUMT blocks based on proximity.
• Taxolotl = Taxolotl: Genome assembly taxonomy summary and assessment tool. Taxolotl combines the MMseqs2 easy-taxonomy with GFF parsing to perform taxonomic analysis of a genome assembly (and any subsets given by taxsubsets=LIST) using an annotated proteome. Taxonomic assignments are mapped onto genes as well as assembly scaffolds and (if assembly=FILE is given) contigs.

Documentation for these tools can be found in their individual repos. Please note that individual repos may be ahead of the main SLiMSuite repo.

More information can also be found in the corresponding publications:

• Chen SH, Rossetto M, van der Merwe M, Lu-Irving P, Yap JS, Sauquet H, Bourke G, Amos TG, Bragg JG & Edwards RJ (accepted): Chromosome-level de novo genome assembly of Telopea speciosissima (New South Wales waratah) using long-reads, linked-reads and Hi-C. Molecular Ecology Resources. [Mol Ecol Res] [bioRxiv]

• Edwards RJ, Field MA, Ferguson JM, Dudchenko O, Keilwagen K, Rosen BD, Johnson GS, Rice ES, Hillier L, Hammond JM, Towarnicki SG, Omer A, Khan R, Skvortsova K, Bogdanovic O, Zammit RA, Aiden EL, Warren WC & Ballard JWO (2021): Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 22:188 [BMC Genomics] [PubMed] [bioRxiv]

• Stuart KC*, Edwards RJ*, Cheng Y, Warren WC, Burt DW, Sherwin WB, Hofmeister NR, Werner SJ, Ball GF, Bateson M, Brandley MC, Buchanan KL, Cassey P, Clayton DF, De Meyer T, Meddle SL & Rollins LA (preprint): Transcript- and annotation-guided genome assembly of the European starling. bioRxiv 2021.04.07.438753; doi: 10.1101/2021.04.07.438753. [*Joint first authors] [bioRxiv]

See also the included release_notes.txt on GitHub for a full list of the python module updates since v1.9.0.

SLiMSuite release v1.9.1 (2020-12-27)

SLiMSuite release v1.9.1 (2020-12-27) is now on GitHub and Zenodo:

• Edwards RJ (2020): SLiMSuite v1.9.1 (2020-12-27). Zenodo DOI: 10.5281/zenodo.3229523

SLiMSuite v1.9 sees the introduction of four genome assembly tools:

• Diploidocus = Diploid genome assembly analysis toolkit. Includes assembly cleanup (haplotig/artefact removal), genome size prediction and read depth copy number analysis.
• PAFScaff = Pairwise mApping Format reference-based scaffold anchoring and super-scaffolding. Uses minimap2 to map a genome assembly onto reference chromosomes.
• SAAGA = Summarise, Annotate & Assess Genome Annotations. Uses a reference proteome to summarise and assess genome annotations.
• SynBad = Synteny-based scaffolding adjustment tool for comparing two related genome assemblies and identify putative translocations and inversions between the two that correspond to gap positions. (Development only.)

There have also been significant updates to:

• BUSCOMP = BUSCO Compiler and Comparison tool. Used for genome assembly completeness estimates that are robust to sequence quality, and for compiling BUSCO results.

Other changes include some initial reformatting for Python3 compatibility. This is ongoing work; please report any odd behaviour.

See the included release_notes.txt for a full list of the python module updates since v1.8.1.

NOTE: At time of posting, the REST servers have not yet been updated with the latest version. This will happen soon.

SLiMSuite release v1.8.1 (2019-05-27)

SLiMSuite release v1.8.1 (2019-05-27) is now on GitHub and Zenodo:

• Edwards RJ (2019): SLiMSuite v1.8.1 (2019-05-27). Zenodo DOI: 10.5281/zenodo.3229523

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. The REST servers have also been updated to run this version of the code.

This release of SLiMSuite contains a number of updates related to the REST servers and some new tools, notably SAMPhaser long read diploid phasing algorithm, and BUSCOMP BUSCO compiler and comparison tool. See release notes (below) for more details.

SLiMSuite updates

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.

SLiMSuite release v1.4.0 (2018-06-02) now oline

SLiMSuite release v1.4.0 (2018-07-02) is now on GitHub. The REST servers have also been updated to run this version of the code.

This release of SLiMSuite contains a number of updates related to the REST servers and some new pre-release dev tools in the main repo (but not the *.tgz file).

SeqList has updated sequence summary statistics and grep-based redundancy removal for large genomes.

One major bug fix is a change to parsing Uniprot entries from the website following a change in behaviour of the API.

SLiMSuite updates

Updates in extras/:

• rje_pydocs: Updated from Version 2.16.3.
→ Version 2.16.4: Tweaked formatDocString.
→ Version 2.16.5: Added general commands to docstring HTML for REST servers.
→ Version 2.16.6: Modified parsing to keep DocString for SPyDarm runs.
→ Version 2.16.7: Fixed T/F/FILE option type parsing bug.

Updates in libraries/:

• rje_blast_V2: Updated from Version 2.18.0.
→ Version 2.19.0: Added blastgz=T/F : Whether to zip and unzip BLAST results files [False]
→ Version 2.19.1: Fixed erroneous i=-1 blastprog over-ride but not sure why it was happening.
→ Version 2.20.0: Added localGFF output
→ Version 2.21.0: Added blasttask=X setting for BLAST -task ['megablast']
→ Version 2.22.0: Added dust filter for blastn and setting blastprog based on blasttask
→ Version 2.22.1: Added trimLocal error catching for exonerate issues.
→ Version 2.22.2: Fixed GFF attribute case issue.

• rje_db: Updated from Version 1.8.6.
→ Version 1.9.0: Added comment output to saveToFile().

• rje_disorder: Updated from Version 0.8.
→ Version 1.0.0: Added random disorder function and elevated to v1.x as fully functional for SLiMSuite
→ Version 1.1.0: Added strict option for disorder method selection. Added minorder=X.
→ Version 1.2.0: Added saving and loading scores to IUScoreDir/.

• rje_gff: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.
→ Version 0.1.0: Basic functional version.

• rje_hpc: Updated from Version 1.1.
→ Version 1.1.1: Added output of subjob command to log as run.

• rje_html: Updated from Version 0.2.1.
→ Version 0.3.0: Added optional loading of javascript files and stupidtable.js?dev default.

• rje_qsub: Updated from Version 1.9.1.
→ Version 1.9.2: Modified qsub() to return job ID.

• rje_samtools: Updated from Version 1.19.2.
→ Version 1.20.0: Added parsing of BAM file - needs samtools on system. Added minsoftclip=X, maxsoftclip=X and minreadlen=X.

• rje_seq: Updated from Version 3.24.0.
→ Version 3.25.0: 9spec=T/F : Whether to treat 9XXXX species codes as actual species (generally higher taxa) [False]

• rje_seqlist: Updated from Version 1.25.0.
→ Version 1.26.0: Updated sequence statistics and fixed N50 underestimation bug.
→ Version 1.26.1: Fixed median length overestimation bug.
→ Version 1.26.2: Fixed sizesort bug. (Now big to small as advertised.)
→ Version 1.27.0: Added grepNR() method (dev only). Switched default to RevCompNR=T.
→ Version 1.28.0: Fixed second pass NR naming bug and added option to switch off altogether.
→ Version 1.29.0: Added maker=T/F : Whether to extract MAKER2 statistics (AED, eAED, QI) from sequence names [False]

• rje_slimcalc: Updated from Version 0.9.3.
→ Version 0.10.0: Added extra disorder methods to slimcalc.

• rje_taxonomy: Updated from Version 1.2.0.
→ Version 1.3.0: taxtable=T/F : Whether to output results in a table rather than text lists [False]

• rje_tree: Updated from Version 2.15.0.
→ Version 2.16.0: 9spec=T/F : Whether to treat 9XXXX species codes as actual species (generally higher taxa) [False]
→ Version 2.16.1: Modified NSF reading to cope with extra information beyond the ";".

• rje_uniprot: Updated from Version 3.24.1.
→ Version 3.24.2: Updated HTTP to HTTPS. Having some download issues with server failures.
→ Version 3.25.0: Fixed new Uniprot batch query URL. Added onebyone=T/F : Whether to download one entry at a time. Slower but should maintain order [False].

• rje_zen: Updated from Version 1.3.2.
→ Version 1.4.0: Added some more words and "They fight crime!" structure.

Updates in tools/:

• gablam: Updated from Version 2.28.3.
→ Version 2.29.0: Added localGFF=T/F output

• gasp: Updated from Version 1.4.
→ Version 2.0.0: Upgraded to rje_obj framework for REST server.

• gasp_V1: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 1.0: Improved version with second pass.
→ Version 1.1: Improved OO. Restriction to descendant AAs. (Good for BAD etc.)
→ Version 1.2: No Out Object in Objects
→ Version 1.3: Added more interactive load options
→ Version 1.4: Minor tweaks to imports.

• gopher: Updated from Version 3.4.2.
→ Version 3.4.3: Added checking and warning if no bootstraps for orthtree.

• haqesac: Updated from Version 1.11.0.
→ Version 1.12.0: 9spec=T/F : Whether to treat 9XXXX species codes as actual species (generally higher taxa) [False]

• multihaq: Updated from Version 1.3.0.
→ Version 1.4.0: Added SLiMFarmer batch forking if autoskip=F and i=-1.
→ Version 1.4.1: Added haqblastdir=PATH: Directory in which MultiHAQ BLAST2FAS BLAST runs will be performed [./HAQBLAST/]

• pagsat: Updated from Version 2.3.3.
→ Version 2.3.4: Fixed full.fas request bug.
→ Version 2.4.0: Added PAGSAT compile mode to generate comparisons of reference chromosomes across assemblies.

• seqsuite: Updated from Version 1.14.0.
→ Version 1.14.1: Added zentest for testing the REST servers.
→ Version 1.15.0: Added GASP to REST servers.
→ Version 1.16.0: Add rje_gff.GFF to REST servers.
→ Version 1.17.0: Added batch summarise mode.
→ Version 1.18.0: Added rje_apollo.Apollo to REST servers.
→ Version 1.19.0: Tweaked the output of batch summarise, adding Gap% and reducing dp for some fields.
→ Version 1.19.1: Fixed GapPC summarise output to be a percentage, not a fraction.

• slimbench: Updated from Version 2.14.0.
→ Version 2.14.1: Fixed up PPIBench results loading.
→ Version 2.14.2: Fixed ByCloud bug.
→ Version 2.15.0: Updated assessSearchMemSaver() to handle different data types properly. dombench not yet supported.
→ Version 2.16.0: Added ppi hub/slim summary and motif filter for assessment datasets post-rating (still count as OT)
→ Version 2.16.1: Bug-fixing PPI generation from pairwise PPI files.
→ Version 2.16.2: Fixed benchmarking setup bug.
→ Version 2.16.3: Fixed bug when Hub-PPI links fail during PPI Benchmarking.
→ Version 2.17.0: Added output of missing datasets when balanced=T.
→ Version 2.18.0: Added dev OccBench with improved ratings and more efficient results handling. (dev only)
→ Version 2.18.1: Added additional OccBench options (bymotif, occsource, occspec)
→ Version 2.18.2: Fixed problem with source file selection ignoring i=-1.

• slimfarmer: Updated from Version 1.7.0.
→ Version 1.8.0: jobforks=X : Number of forks to pass to farmed out run if >0 [0]
→ Version 1.9.0: daisychain=X : Chain together a set of qsub runs of the same call that depend on the previous job.

• slimfinder: Updated from Version 5.3.3.
→ Version 5.3.4: Fixed terminal (^/$) musthave bug.

• slimsuite: Updated from Version 1.7.0.
→ Version 1.7.1: Added error raising for protected REST alias data.

• smrtscape: Updated from Version 2.2.1.
→ Version 2.2.2: Added dna=T to all SeqList object generation.

• snapper: Updated from Version 1.6.0.
→ Version 1.6.1: Fixed bug for reducing to unique-unique pairings that was over-filtering.

---

© RJ Edwards 2018. Last modified 2 Jul 2018.

SLiMSuite REST server is back up

The REST server is back up. The development server is currently having an upgrade and should not be used.

SLiMSuite REST Servers updated

The SLiMSuite REST Servers have been updated to the latest release code (v1.3.0). Please report any issues!

SLiMSuite release v1.3.0 (2017-12-18) online

SLiMSuite release v1.3.0 (2017-12-18) is now on GitHub. Funding for SLiMSuite development is proving elusive at present, so this release is a little less organised (and later) than planned. The main additions are various programs in development for PacBio genomics and a draft SLiMSuite parser Shiny app in the new shiny/ directory. The old packages/ directory has also been removed. Check the docs/release/ files and see below for more information on this release.

Another release with improved documentation is currently planned for early 2018. As ever, if you want access to the latest code, email to download the full svn repository.

SLiMSuite updates

Updates in extras/:

• rje_dbase: Updated from Version 2.3.
→ Version 2.3.1: Updated the dbdownload function to recognise individual files and wildcard file lists.

• rje_pydocs: Updated from Version 2.16.3.
→ Version 2.17.4: Tweaked formatDocString.
→ Version 2.17.5: Added general commands to docstring HTML for REST servers.

Updates in legacy/:

Updates in libraries/:

• rje: Updated from Version 4.17.0.
→ Version 4.18.0: Added Roman numeral functions.
→ Version 4.18.1: Updated error handling for full REST output.
→ Version 4.18.2: Fixed rje module call bug.
→ Version 4.19.0: Tweaked Docstring. Added extra parameter catching. Added report of INI loading.

• rje_blast_V2: Updated from Version 2.11.2.
→ Version 2.12.0: Added localidcut %identity filter for GABLAM calculations.
→ Version 2.13.0: Added GFF and SAM output for BLAST local tables for GABLAM, PAGSAT etc.
→ Version 2.14.0: Updated gablamfrag=X and fragmerge=X usage. Fixed localFragFas position output.
→ Version 2.15.0: Fragmerge no longer removes flanks and can be negative for enforced overlap!
→ Version 2.16.0: Added qassemblefas mode for generating fasta file from outfmt 4 run.
→ Version 2.16.1: Improved error messages for BLAST QAssembly.
→ Version 2.17.0: qconsensus=X : Whether to convert QAssemble alignments to consensus sequences (None/Hit/Full) [None]
→ Version 2.17.1: Modified QAssembleFas output sequence names for better combining of hits. Added QFasDir.
→ Version 2.17.2: Modified QAssembleFas output file names for better re-running. Fixed major QConsensus Bug.
→ Version 2.18.0: Added REST output. Fixed QConsensus=Full bug.

• rje_db: Updated from Version 1.8.1.
→ Version 1.8.2: Fixed minor readSet bug.
→ Version 1.8.3: Minor debugging message changes.
→ Version 1.8.4: Cosmetic log message changes.
→ Version 1.8.5: Added saveToFileName() function.
→ Version 1.8.6: Minor IndexReport tweak.

• rje_genbank: Updated from Version 1.5.2.
→ Version 1.5.3: Fixed https genbank download issue.

• rje_menu: Updated from Version 0.4.0.
→ Version 0.5.0: Enabled simpler return tuples.

• rje_obj: Updated from Version 2.2.1.
→ Version 2.2.2: Updated error handling for full REST output.

• rje_qsub: Updated from Version 1.6.3.
→ Version 1.7.0: Added option for email when job started
→ Version 1.8.0: Added modpurge=T/F : Whether to purge loaded modules in qsub job file prior to loading [True]
→ Version 1.9.0: Added precall=LIST : List of additional commands to run between module loading and program call []
→ Version 1.9.1: Removed default module list: causing conflicts. Better to have in INI file.

• rje_samtools: Updated from Version 1.8.1.
→ Version 1.9.0: Added depthplot data generation. (Will need to add R function for plot itself.)
→ Version 1.9.1: Changed mincut default to 0.1.
→ Version 1.10.0: Added readlen output, which is like the depth plot but uses max read length (kb) instead of depth.
→ Version 1.11.0: Added dirnlen=X : Include directional read length data at X bp intervals (depthplot=T; 0=OFF) [500]
→ Version 1.11.1: Minor tweaks to try and speed up pileup parsing.
→ Version 1.12.0: Updated the snpfreq run code to make clearer and check for parsing issues. Set mincut=1 default.
→ Version 1.13.0: Added skiploci=LIST - need to screen out mitochondrion from Illumina Pileup parsing!
→ Version 1.14.0: Added forking of pileup parsing for SNPFreq analysis.
→ Version 1.14.1: Fixed SNPFreq rerunning bug.
→ Version 1.15.0: Added rgraphics=T/F : Whether to generate snpfreq multichromosome plots [True]
→ Version 1.16.0: Add coverage calculation per locus to depth plot table output (depthplot=T).
→ Version 1.16.1: Added reporting of existing files for parsing Pileup.
→ Version 1.17.0: Added parsing of lengths from SAM files to RID file.
→ Version 1.18.0: Updated processing of Treatment and Control without Alt to still limit to SNPTable. Fixed SNPFreq filters.
→ Version 1.19.0: snptableout=T/F : Output filtered alleles to SNP Table [False]
→ Version 1.19.1: Fixed AltLocus SNP table bug.
→ Version 1.19.2: Updated forker parsing to hopefully fix bug.

• rje_seqlist: Updated from Version 1.20.1.
→ Version 1.21.0: Added capacity to add/update database object from self.summarise() even if not seqmode=db. Added filedb mode.
→ Version 1.22.0: Added geneDic() method.
→ Version 1.23.0: Added seqSequence() method.
→ Version 1.24.0: Add NNN gaps option and "delete rest of sequences" to edit().
→ Version 1.24.1: Minor edit bug fix and DNA toggle option.
→ Version 1.25.0: Added loading of FASTQ files in seqmode=file mode.

• rje_sequence: Updated from Version 2.5.3.
→ Version 2.6.0: Added mutation dictionary to Ks calculation.

• rje_slim: Updated from Version 1.12.0.
→ Version 1.12.1: Modified error message.

• rje_slimcalc: Updated from Version 0.9.2.
→ Version 0.9.3: Changed fudge error to warning.

• rje_slimcore: Updated from Version 2.7.7.
→ Version 2.7.8: Fixed batch=FILE error for single input files.
→ Version 2.8.0: Added map and failed output to REST servers and standalone uniprotid=LIST input runs.
→ Version 2.8.1: Updated resfile to be set by basefile if no resfile=X setting given
→ Version 2.9.0: Added separate IUPred long suffix for reusing predictions

• rje_synteny: Updated from Version 0.0.0.
→ Version 0.0.1: Altered problematic ValueError to warnLog()
→ Version 0.0.2: Updated the synteny mappings to be m::n instead of m:n for Excel compatibility.
→ Version 0.0.3: Added catching of the Feature locus/accnum mismatch issue.

• rje_tree: Updated from Version 2.14.0.
→ Version 2.14.1: Fixed clustalw2 makeTree issue.
→ Version 2.15.0: Added IQTree.

• rje_uniprot: Updated from Version 3.22.0.
→ Version 3.23.0: Added accnum map table output. Fixed REST output bug when bad IDs given. Added version and about output.
→ Version 3.24.0: Added pfam out and changed map table headers.
→ Version 3.24.1: Fixed process Uniprot error when uniprot=FILE given.

• rje_zen: Updated from Version 1.3.1.
→ Version 1.3.2: Added some more words.

• snp_mapper: Updated from Version 1.0.0.
→ Version 1.1.0: Added pNS and modified the "Positive" CDS rating to be pNS < 0.05.
→ Version 1.1.1: Updated pNS calculation to include EXT mutations and substitution frequency.
→ Version 1.2.0: SNPByFType=T/F : Whether to output mapped SNPs by feature type (before FTBest filtering) [False]

Updates in tools/:

• gablam: Updated from Version 2.23.0.
→ Version 2.23.1: Added tuplekeys=T to cmd_list as default. (Can still be over-ridden if it breaks things!)
→ Version 2.24.0: Added localidmin and and localidcut as %identity versions of localmin and localcut. (Use for PAGSAT.)
→ Version 2.25.0: Added localsAM=T/F : Save local (and unique) hits data as SAM files in addition to TDT [False]
→ Version 2.26.0: Fixed fragfas output and clarified fullblast=T/F, localmin=X and localcut=X. Set fullblast=T keepblast=T.
→ Version 2.26.1: Fixed keepblast error.
→ Version 2.26.2: Fixed gablamcut fragfas filtering bug.
→ Version 2.26.3: Fixed nrseq=T to use Query OR Hit stat for NR filtering.
→ Version 2.26.4: Minor bug fix to nrchoice command parsing.
→ Version 2.27.0: Fragmerge no longer removes flanks and can be negative for enforced overlap!
→ Version 2.28.0: Added localidmin=PERC to localUnique (and thus Snapper).
→ Version 2.28.1: Fixed missing combinedfas when using existing blastres.
→ Version 2.28.2: Minor bug fix for NRSeq manual choice when i=-1.
→ Version 2.28.3: Fixed NRSeq query sorting bug.

• haqesac: Updated from Version 1.10.2.
→ Version 1.10.3: Added catching of bad query when i=-1.
→ Version 1.11.0: Added resdir=PATH [./HAQESAC/] for d>0 outputs.

• multihaq: Updated from Version 1.2.2.
→ Version 1.3.0: MultiCut : Restrict BLAST to the top X hits from each database [100]

• pagsat: Updated from Version 1.11.2.
→ Version 1.11.3: Added reference=FILE as alias for refgenome=FILE. Fixed orphan delete bug.
→ Version 1.12.0: Tidying up and documenting outputs. Changed default minloclen=250 and minlocid=95. (LTR identification.)
→ Version 2.0.0: Major overhaul of outputs to improve consistency and clarity. Added Snapper to main run.
→ Version 2.1.0: Added localSAM output.
→ Version 2.1.1: Fixed the case of some output files.
→ Version 2.1.2: Fixed some issues with reverse hits in Snapper and application of minlocid.
→ Version 2.2.0: Added mapout=T, which is recommended for first run if going to subsequently tidy. (Run tidy on mapfile.)
→ Version 2.2.1: Tried to fix covplot bug in compare=FILES mode.
→ Version 2.2.2: Cleaned up *.map.* output for SAMPhaser output files. Added tidy/mapfas option selection.
→ Version 2.2.3: Added #NOTE to tidy and fixed makesnp=T bug.
→ Version 2.2.4: Fixed `fragrevcomp=F` bug for Gene and Protein TopHits.
→ Version 2.2.5: Hopefully really fixed makesnp=T bug now!
→ Version 2.2.6: Fixed Haploid tidy sequence output naming bug.
→ Version 2.2.7: Fixed Compare File path bug & dropped some empty outputs.
→ Version 2.3.0: Minor bug fixes and extra tidy options (join gaps and multi-deletes).
→ Version 2.3.1: Minor bug fixes.
→ Version 2.3.2: Updated the synteny mappings to be m::n instead of m:n for Excel compatibility.
→ Version 2.3.3: Fixed bad assembly sequence name bug.

• pagsat_V1: Created/Renamed/moved.
→ Version 1.0.0: Initial working version for based on rje_pacbio assessment=T.
→ Version 1.1.0: Fixed bug with gene and protein summary data. Removed gene/protein reciprocal searches. Added compare mode.
→ Version 1.1.1: Added PAGSAT output directory for tidiness!
→ Version 1.1.2: Renamed the PacBio class PAGSAT.
→ Version 1.2.0: Tidied up output directories. Added QV filter and Top Gene/Protein hits output.
→ Version 1.2.1: Added casefilter=T/F : Whether to filter leading/trailing lower case (low QV) sequences [True]
→ Version 1.3.0: Added tophitbuffer=X and initial synteny analysis for keeping best reference hits.
→ Version 1.4.0: Added chrom-v-contig alignment files along with *.ordered.fas.
→ Version 1.4.1: Made default chromalign=T.
→ Version 1.4.2: Fixed casefilter=F.
→ Version 1.5.0: diploid=T/F : Whether to treat assembly as a diploid [False]
→ Version 1.6.0: mincontiglen=X : Minimum contig length to retain in assembly [1000]
→ Version 1.6.1: Added diploid=T/F to R PNG call.
→ Version 1.7.0: Added tidy=T/F option. (Development)
→ Version 1.7.1: Updated tidy=T/F to include initial assembly.
→ Version 1.7.2: Fixed some bugs introduced by changing gablam fragment output.
→ Version 1.7.3: Added circularise sequence generation.
→ Version 1.8.0: Added orphan processing and non-chr naming of Reference.
&r

Edwards Lab: The SLiMEnrich Shiny App is now live

Edwards Lab: The SLiMEnrich Shiny App is now live: Sobia ’s first Shiny App is now up and running for final pre-publication testing on our new EdwardsLab RShiny server. See post for details.

Problem with SLiMFinder bioware webserver

There is currently a problem with the SLiMFinder webserver hosted at UCD, where masking is failing to be performed, regardless of settings. This severely impacts the quality of results. (Disorder, low complexity and n-terminal methionine masking are generally recommended for SLiMFinder.)

I am in communication with the Shields lab to try and get the issue fixed but, until it has been rectified, the bioware.ucd.ie SLiMFinder webserver should not be used.

If you wish to run SLiMFinder online, you can do so via the SLiMFinder REST server (see BioInfoSummer 2016 workshop), which can also be run from within Cytoscape using the SLiMScape App.

SLiMSuite release v1.2.0 (2016-09-12) online

The long-overdue September 2016 release of SLiMSuite 2016-09-12 - v1.2.0 is now on GitHub. Apart from a few bug fixes, the main updates in this release are to the tools for PacBio genomics, notably PAGSAT, SMRTSCAPE and a new SNP Mapping tool, Snapper. These are still in development and need further documentation but are ready for use with a little help. Please get in touch if you are interested. Proper documentation and example use will hopefully follow soon, as the first PacBio yeast paper is written.

GABLAM has had some minor tweaks for improved function with Snapper, PAGSAT and another developmental tool that will be in the next release (REVERT - available via the REST servers). These have been focused on the fragfas=T output of fragmented BLAST hits based on local alignments. This includes addition of a new default to reverse complement reverse hits (fragrevcomp=T) and the separation of parameters for splitting up local hits into multiple fragments (gablamfrag=X) and merging close/overlapping fragments (fragmerge=X).

SLiMSuite updates in this release

Updates in extras/:

• rje_pydocs: Updated from Version 2.16.2.
→ Version 2.16.3: Fixed docstring REST parsing to work with _V* modules.

Updates in libraries/:

• rje: Updated from Version 4.15.1.
→ Version 4.16.0: Added list2dict(inlist,inkeys) and dict2list(indict,inkeys) functions.
→ Version 4.16.1: Improved handling of integer parameters when given bad commands.
→ Version 4.17.0: Added extra functions to randomList()

• rje_blast_V2: Updated from Version 2.9.1.
→ Version 2.10.0: Added nocoverage calculation based on local alignment table.
→ Version 2.11.0: Added localFragFas output method.
→ Version 2.11.1: Fixed snp local table revcomp bug. [Check this!]
→ Version 2.11.2: Fixed GABLAM calculation bug when '*' in protein sequences.

• rje_db: Updated from Version 1.8.0.
→ Version 1.8.1: Added sfdict to saveTable output.

• rje_genbank: Updated from Version 1.3.2.
→ Version 1.4.0: Added addtags=T/F : Add locus_tag identifiers if missing - needed for gene/cds/prot fasta output [False]
→ Version 1.4.1: Fixed genetic code warning.
→ Version 1.5.0: Added setupRefGenome() method based on PAGSAT code.
→ Version 1.5.1: Fixed logskip append locus sequence file bug.
→ Version 1.5.2: Fixed addtag(s) bug.

• rje_hprd: Updated from Version 1.2.
→ Version 1.2.1: Fixed "PROTEIN_ARCHITECTURE" bug.

• rje_menu: Updated from Version 0.3.
→ Version 0.4.0: Changed handling of default for exiting menu loop. May affect behaviour of some existing menus.

• rje_mitab: Updated from Version 0.2.0.
→ Version 0.2.1: Fixed redundant evidence/itype bug (primarily dip)

• rje_obj: Updated from Version 2.1.3.
→ Version 2.2.0: Added screenwrap=X.
→ Version 2.2.1: Improved handling of integer parameters when given bad commands.

• rje_samtools: Updated from Version 0.1.0.
→ Version 0.2.0: Added majmut=T/F : Whether to restrict output and stats to positions with non-reference Major Allele [False]
→ Version 1.0.0: Major reworking. Old version frozen as rje_samtools_V0.
→ Version 1.1.0: Added snptabmap=X,Y alternative SNPTable mapping and read_depth statistics []. Added majref=T/F.
→ Version 1.2.0: Added developmental combining of read mapping onto two different genomes.
→ Version 1.3.0: Major debugging and code clean up.
→ Version 1.4.0: Added parsing of read number (to link SNPs) and fixed deletion error at same time. Added rid=T/F and snponly=T/F.
→ Version 1.5.0: Added biallelic=T/F : Whether to restrict SNPs to pure biallelic SNPs (two alleles meeting mincut) [False]
→ Version 1.5.1: Fixed REF/Ref ALT/Alt bug.
→ Version 1.6.0: Added majfocus=T/F : Whether the focus is on Major Alleles (True) or Mutant/Reference Alleles (False) [True]
→ Version 1.7.0: Added parsing of *.sam files for generating RID table.
→ Version 1.8.0: Added read coverage summary/checks.
→ Version 1.8.1: Fixed issue when RID file not generated by pileup parsing. Set RID=True by default to avoid issues.

• rje_samtools_V0: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 0.1.0: Modified version to handle multiple loci per file. (Original was for single bacterial chromosomes.)
→ Version 0.2.0: Added majmut=T/F : Whether to restrict output and stats to positions with non-reference Major Allele [False]

• rje_seq: Updated from Version 3.23.0.
→ Version 3.24.0: Added REST seqout output.

• rje_seqlist: Updated from Version 1.15.3.
→ Version 1.15.4: Fixed REST server output bug.
→ Version 1.15.5: Fixed reformat=fasta default issue introduced from fixing REST output bug.
→ Version 1.16.0: Added edit=T sequence edit mode upon loading (will switch seqmode=list).
→ Version 1.17.0: Added additional summarise=T output for seqmode=db.
→ Version 1.18.0: Added revcomp to reformat options.
→ Version 1.19.0: Added option log description for deleting sequence during edit.
→ Version 1.20.0: Added option to give a file of changes for edit mode.
→ Version 1.20.1: Fixed edit=FILE deletion bug.

• rje_sequence: Updated from Version 2.5.2.
→ Version 2.5.3: Fixed genetic code warning error.

• rje_slimcore: Updated from Version 2.7.5.
→ Version 2.7.6: Added feature masking log info or warning.
→ Version 2.7.7: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour.

• rje_synteny: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.

• rje_taxonomy: Updated from Version 1.1.0.
→ Version 1.2.0: Added storage of Parents.

• rje_tree: Updated from Version 2.13.0.
→ Version 2.14.0: Added cladeSpec().

• rje_uniprot: Updated from Version 3.21.4.
→ Version 3.22.0: Tweaked REST table output.

• rje_xref: Updated from Version 1.8.0.
→ Version 1.8.1: Added rest run mode to avoid XRef table output if no gene ID list is given. Added `genes` and `genelist` as `idlist=LIST` synonym.
→ Version 1.8.2: Catching self.dict['Mapping'] error for REST server.

• snp_mapper: Updated from Version 0.4.0.
→ Version 0.5.0: Added CDS rating.
→ Version 0.6.0: Added AltFT mapping mode (map features to AltLocus and AltPos)
→ Version 0.7.0: Added additional fields for processing Snapper output. (Hopefully will still work for SAMTools etc.)
→ Version 0.8.0: Added parsing of GFF file from Prokka.
→ Version 0.8.1: Corrected "intron" classification for first position of features. Updated FTBest defaults.
→ Version 1.0.0: Version that works with Snapper V1.0.0. Not really designed for standalone running any more.

Updates in tools/:

• comparimotif_V3: Updated from Version 3.12.
→ Version 3.13.0: Added REST server function.

• gablam: Updated from Version 2.20.0.
→ Version 2.21.0: Added nocoverage Table output of regions missing from pairwise SNP Table.
→ Version 2.21.1: Added fragrevcomp=T/F : Whether to reverse-complement DNA fragments that are on reverse strand to query [True]
→ Version 2.22.0: Added description to HitSum table.
→ Version 2.22.1: Added localaln=T/F to keep local alignment sequences in the BLAST local Table.
→ Version 2.22.2: Fixed local output error. (Query/Qry issue - need to fix this and make consistent!)
→ Version 2.22.3: Fixed blastv and blastb error: limit also applies to individual pairwise hits!
→ Version 2.23.0: Divided GablamFrag and FragMerge.

• pagsat: Updated from Version 1.6.1.
→ Version 1.7.0: Added tidy=T/F option. (Development)
→ Version 1.7.1: Updated tidy=T/F to include initial assembly.
→ Version 1.7.2: Fixed some bugs introduced by changing gablam fragment output.
→ Version 1.7.3: Added circularise sequence generation.
→ Version 1.8.0: Added orphan processing and non-chr naming of Reference.
→ Version 1.9.0: Modified the join sorting and merging. Added better tracking of positions when trimming.
→ Version 1.9.1: Added joinmargin=X : Number of extra bases allowed to still be considered an end local BLAST hit [10]
→ Version 1.10.0: Added weighted tree output and removed report warning.
→ Version 1.10.1: Fixed issue related to having Description in GABLAM HitSum tables.
→ Version 1.10.2: Tweaked haploid core output.
→ Version 1.10.3: Fixed tidy bug for RevComp contigs and switched joinsort default to Identity. (Needs testing.)
→ Version 1.10.4: Added genetar option to tidy out genesummary and protsummary output. Incorporated rje_synteny.
→ Version 1.10.5: Set gablamfrag=1 for gene/protein hits.
→ Version 1.11.0: Consolidated automated tidy mode and cleaned up some excess code.
→ Version 1.11.1: Added option for running self-PAGSAT of ctidX contigs versus haploid set. Replaced ctid "X" with "N".
→ Version 1.11.2: Fixed Snapper run choice bug.

• pingu_V4: Updated from Version 4.5.3.
→ Version 4.6.0: Added hubonly=T/F : Whether to restrict pairwise PPI to those with both hub and spoke in hublist [False]
→ Version 4.6.1: Fixed some ppifas=T/F bugs and added combineppi=T/F : Whether to combine all spokes into a single fasta file [False]
→ Version 4.6.2: Added check/filter for multiple SpokeUni pointing to same sequence. (Compilation redundancy mapping failure!)
→ Version 4.6.3: Fixed issue with 1:many SpokeUni:Spoke mappings messing up XHub.
→ Version 4.7.0: Added ppidbreport=T/F : Summary output for PPI compilation of evidence/PPIType/DB overlaps [True]
→ Version 4.8.0: Fixed report duplication issue and added additional summary output

• qslimfinder: Updated from Version 2.1.0.
→ Version 2.1.1: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour.

• seqsuite: Updated from Version 1.11.0.
→ Version 1.11.1: Redirected PacBio to call SMRTSCAPE.
→ Version 1.11.2: Fixed batchrun batchlog=False log error.
→ Version 1.12.0: Added Snapper.

• slimfarmer: Updated from Version 1.4.3.
→ Version 1.4.4: Modified default vmem request to 126GB from 127GB.
→ Version 1.4.5: Updated BLAST loading default to 2.2.31

• slimfinder: Updated from Version 5.2.1.
→ Version 5.2.2: Added warnings for ambocc and minocc that exceed the absolute minima. Updated docstring.
→ Version 5.2.3: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour. Fixed FTMask=T/F bug.

• slimparser: Updated from Version 0.3.3.
→ Version 0.3.4: Tweaked error messages.
→ Version 0.4.0: Added simple json format output.

• slimprob: Updated from Version 2.2.4.
→ Version 2.2.5: Fixed FTMask=T/F bug.

• slimsearch: Updated from Version 1.7.
→ Version 1.7.1: Minor modification to docstring. Preparation for update to SLiMSearch 2.0 optimised for proteome searches.

• slimsuite: Updated from Version 1.5.1.
→ Version 1.5.2: Updated XRef REST call.
→ Version 1.6.0: Removed SLiMCore as default. Default will now show help.

• smrtscape: Updated from Version 1.8.0.
→ Version 1.9.0: Updated empirical preassembly mapefficiency calculation.
→ Version 1.10.0: Added batch processing of subread files.
→ Version 1.10.1: Fixed bug in batch processing.

• snapper: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.
→ Version 0.1.0: Tidied up with improved run pickup.
→ Version 0.2.0: Added FASTQ and improved CNV output along with all features.
→ Version 0.2.1: Fixed local output error. (Query/Qry issue - need to fix this and make consistent!) Fixed snp local table revcomp bug.
→ Version 0.2.2: Corrected excess CNV table output (accnum AND shortname).
→ Version 0.2.3: Corrected "intron" classification for first position of features. Updated FTBest defaults.
→ Version 1.0.0: Working version with completed draft manual. Added to SeqSuite.
→ Version 1.0.1: Fixed issues when features missing.

New SLiMSuite REST Servers

Since the move to UNSW in 2013, the Bioware SLiMSuite servers and REST servers have been undergoing some much needed TLC. As part of this process, a new set of UNSW REST servers were introduced and online with the 2015-06-01 SLiMSuite release.

An overview of how the REST servers work is given on the REST Homepage. The available tools are listed at the REST Tools page. The main ones - accessible through the SLiMScape app for Cytoscape are (or support):

• SLiMFinder de novo SLiM discovery.
• QSLiMFinder query-focused de novo SLiM discovery.
• SLiMProb defined/known SLiM prediction.
• SLiMMaker Simple Regex SLiM generation from peptides.

The primary focus has been setting up new servers to be accessed via a RESTful-style interface whereby a URL can be directly given to the server and used to either download results directly (if accessing programmatically) or view in a web browser. As with the main programs, these servers use plain text inputs and outputs wherever. Whilst this probably makes proper computer scientists very unhappy, it should make it very easy to incorporate SLiMSuite REST functions into your own scripts - you only need to learn how to parse text. (It also makes it easy for me to swap input sources.) If you don’t want to write your own, SLiMParser is provided in the SLiMSuite download to do this for you.

The other design consideration that has gone into the REST servers is to make them run as much like the commandline versions as possible: (1) they use the same code; (2) they use the same commandline options, parsed from the URL. This means that (a) you should easily be able to reproduce server results on your own system, and (b) new functions (and bug fixes) should become quickly available via the REST servers.

To save the need for constructing complex URLs, there is a simple on-size-fits-all form at the EdwardsLab server page. Over time, tool-specific forms will be established. Currently, this only exists for SLiMMaker.

As ever, if something about the new servers misbehaves or does not make sense - or you really want some new functions - please get in touch.

SLiMSuite release v1.1.0 (2015-11-30) online

The November 2015 release of SLiMSuite v1.1.0 (2015-11-30) in now on GitHub. This is intermediate release in preparation for the BioInfoSummer 2015 SLiMSuite workshop and contains a few minor modifications to SLiMSuite programs. The main updates are preliminary versions of some tools for PacBio genomics, notably PAGSAT and SMRTSCAPE. These are still in development and need further documentation and testing before use is advised.

The SeqSuite Genbank parser has some bug fixes for reverse complemented protein sequences with introns, and initial capacity for different codon tables. (This has been implemented for yeast, so only NCBI transl_tables 1-3 currently implemented: please get in touch if you want to use this program with other codon tables.)

SLiMSuite updates in this release

Updates in libraries/:

• rje: Updated from Version 4.14.0.
→ Version 4.14.1: Fixed matchExp method to be able to handline multilines. (Shame re.DOTALL doesn’t work!)
→ Version 4.14.2: Modified integer commands to read/convert floats.
→ Version 4.15.0: Added intList() and numList() functions.

• rje_db: Updated from Version 1.7.5.
→ Version 1.7.6: Added table.opt[‘Formatted’] = Whether table data has been successfully formatted using self.dataFormat()
→ Version 1.7.7: Added option to constrain table splitting to certain field values.
→ Version 1.8.0: Added option to store keys as tuples for correct sorting. (Make default at some point.)

• rje_genbank: Updated from Version 1.3.1.
→ Version 1.3.2: Fixed bug in reverse complement sequences with introns.

• rje_iridis: Updated from Version 1.10.
→ Version 1.10.1: Attempted to fix SLiMFarmer batch run problem. (Should not be setting irun=batch!)
→ Version 1.10.2: Trying to clean up unknown 30s pause. Might be freemem issue?

• rje_obj: Updated from Version 2.1.2.
→ Version 2.1.3: Modified integer commands to read/convert floats.

• rje_qsub: Updated from Version 1.6.2.
→ Version 1.6.3: Tweaked the showstart command for katana.

• rje_samtools: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 0.1.0: Modified version to handle multiple loci per file. (Original was for single bacterial chromosomes.)

• rje_seqlist: Updated from Version 1.11.0.
→ Version 1.12.0: Added peptides/qregion reformatting and region=X,Y.
→ Version 1.13.0: Added summarise=T option for generating some summary statistics for sequence data. Added minlen & maxlen.
→ Version 1.14.0: Added splitseq=X split output sequence file according to X (gene/species) [None]
→ Version 1.15.0: Added names() method.
→ Version 1.15.1: Fixed bug with storage and return of summary stats.
→ Version 1.15.2: Fixed dna2prot reformatting.
→ Version 1.15.3: Fixed summarise bug (n=1).

• rje_sequence: Updated from Version 2.4.1.
→ Version 2.5.0: Added yeast genome renaming.
→ Version 2.5.1: Modified reverse complement code.
→ Version 2.5.2: Tried to speed up dna2prot code.

• rje_slimcalc: Updated from Version 0.9.
→ Version 0.9.1: Modified combining of motif stats to handle expectString format for individual values.
→ Version 0.9.2: Changed default conscore in docstring to RLC.

• rje_slimcore: Updated from Version 2.7.3.
→ Version 2.7.4: Fixed walltime server bug.
→ Version 2.7.5: Fixed feature masking.

• rje_slimlist: Updated from Version 1.7.2.
→ Version 1.7.3: Fixed bug that could not accept variable length motifs from commandline. Improved error message.

• rje_taxonomy: Updated from Version 1.0.
→ Version 1.1.0: Added parsing of yeast strains.

• rje_tree: Updated from Version 2.11.2.
→ Version 2.12.0: Added treeLen() method.
→ Version 2.13.0: Updated PNG saving with R to use newer code.

• rje_uniprot: Updated from Version 3.21.3.
→ Version 3.21.4: Fixed Feature masking. Should this be switched off by default?

• rje_xref: Updated from Version 1.6.0.
→ Version 1.7.0: Added comments=LIST ist of comment line prefixes marking lines to ignore (throughout file) [‘//’,’%’]
→ Version 1.7.1: Added xreformat=T/F : Whether to apply field reformatting to input xrefdata (True) or just xrefs to map (False) [False]
→ Version 1.8.0: Added recognition and parsing of yeast.txt XRef file from Uniprot (http://www.uniprot.org/docs/yeast.txt)

• snp_mapper: Created/Renamed/moved.
→ Version 0.0: Initial Compilation. Batch mode for mapping SNPs needs updating.
→ Version 0.1: SNP mapping against a GenBank file.
→ Version 0.2: Fixed complement strand bug.
→ Version 0.3.0: Updated to work with RATT(/Mummer?) snp output file. Improved docs.
→ Version 0.4.0: Major reworking for easier updates and added functionality. (Convert to 1.0.0 when complete.)

Updates in tools/:

• gablam: Updated from Version 2.19.2.
→ Version 2.20.0: Added SNP Table output.

• gopher: Updated from Version 3.4.1.
→ Version 3.4.2: Removed GOPHER System Exit on IOError to prevent breaking of REST server.

• pagsat: Created/Renamed/moved.
→ Version 1.0.0: Initial working version for based on rje_pacbio assessment=T.
→ Version 1.1.0: Fixed bug with gene and protein summary data. Removed gene/protein reciprocal searches. Added compare mode.
→ Version 1.1.1: Added PAGSAT output directory for tidiness!
→ Version 1.1.2: Renamed the PacBio class PAGSAT.
→ Version 1.2.0: Tidied up output directories. Added QV filter and Top Gene/Protein hits output.
→ Version 1.2.1: Added casefilter=T/F : Whether to filter leading/trailing lower case (low QV) sequences [True]
→ Version 1.3.0: Added tophitbuffer=X and initial synteny analysis for keeping best reference hits.
→ Version 1.4.0: Added chrom-v-contig alignment files along with *.ordered.fas.
→ Version 1.4.1: Made default chromalign=T.
→ Version 1.4.2: Fixed casefilter=F.
→ Version 1.5.0: diploid=T/F : Whether to treat assembly as a diploid [False]
→ Version 1.6.0: mincontiglen=X : Minimum contig length to retain in assembly [1000]
→ Version 1.6.1: Added diploid=T/F to R PNG call.

• peptcluster: Updated from Version 1.5.1.
→ Version 1.5.2: Improved clarity of warning message.

• pingu_V4: Updated from Version 4.5.0.
→ Version 4.5.1: Debugging missing identifiers and indexing speed. Added good and bad DB.
→ Version 4.5.2: Fixed SIF output and changed names to sif-* for opening in browser.
→ Version 4.5.3: Updated REST output.

• seqsuite: Updated from Version 1.8.0.
→ Version 1.9.0: Added PAGSAT and SMRTSCAPE.
→ Version 1.9.1: Fixed HAQESAC setobjects=True error.
→ Version 1.10.0: Added batchrun=FILELIST batcharg=X batch running mode.
→ Version 1.11.0: Added SAMTools and Snapper/SNP_Mapper.

• slimbench: Updated from Version 2.10.0.
→ Version 2.10.1: Updated ELM Source URLs.

• slimfarmer: Updated from Version 1.4.2.
→ Version 1.4.3: Added recognition of missing slimsuite programs and switching to slimsuite=F.

• slimfinder: Updated from Version 5.2.0.
→ Version 5.2.1: Fixed ambocc<1 and minocc<1 issue. (Using integers rather than floats.) Fixed OccRes Sig output format.

• slimparser: Updated from Version 0.3.1.
→ Version 0.3.2: Fixed issue reading files for full output.
→ Version 0.3.3: Tidied output names when restbase=jobid.

• slimprob: Updated from Version 2.2.3.
→ Version 2.2.4: Improved slimcalc output (s.f.).

• slimsuite: Updated from Version 1.5.0.
→ Version 1.5.1: Changed disorder to iuscore to avoid module conflict.

• smrtscape: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.
→ Version 1.0.0: Initial working version for server.
→ Version 1.1.0: Added xnlist=LIST : Additional columns giving % sites with coverage >= Xn [10,25,50,100].
→ Version 1.2.0: Added assessment -> now PAGSAT.
→ Version 1.3.0: Added seed and anchor read coverage generator (calculate=T).
→ Version 1.3.1: Deleted assessment function. (Now handled by PAGSAT.)
→ Version 1.4.0: Added new coverage=T function that incorporates seed and anchor subreads.
→ Version 1.5.0: Added parseparam=FILES with paramlist=LIST to parse restricted sets of parameters.
→ Version 1.6.0: New SMRTSCAPE program building on PacBio v1.5.0. Added predict=T/F option.
→ Version 1.6.1: Updated parameters=T to incorporate that the seed read counts as X=1.
→ Version 1.7.0: Added *.summary.tdt output from subread summary analysis. Added minreadlen.
→ Version 1.8.0: preassembly=FILE: Preassembly fasta file to assess/correct over-fragmentation (use seqin=FILE for subreads)

SLiMSuite release 2015-06-01 now available

A new download of SLiMSuite (release 2015-06-01) is now available. This is the first release in the new git repository at https://github.com/slimsuite/SLiMSuite. A tarball slimsuite.2015-06-01.tgz is also available, containing the same code. Once unpacked, it should be possible to pull down additional updates with git. (This release corresponds to the UCD svn repo r895.)

The major change since the last release is a general tidying of the repository in preparation for going on GitHub and tidying documentation for the new online help via the SLiMSuite REST Server:

for:

To try out the new documentation for a given program, replace sitemap in the box and click View Documentation. Leaving sitemap in the box will list all modules, which can then be clicked on.

The old PDF Manuals are still included in the release and can be accessed from the EdwardsLab Software page. These will be updated eventually but the focus is currently on getting module docstrings and the online help up-to-date. As ever, please get in touch if you have any questions.

This release also sees the addition of a new tool, SLiMParser for running/parsing the new REST servers. SLiMMaker has also undergone some improvements and now features: (1) basic peptide alignment prior to motif generation; (2) extension of degenerate sites using an “equivalence” list of similar amino acids.

A full list of updates is given below.

Updates since previous release

Updates in tools/:

• gablam: Updated from Version 2.16.1.
→ Version 2.17.0: Added localalnfas=T/F : Whether to output local alignments to *.local.fas fasta file (if local=T) [False]
→ Version 2.17.1: Fixed bug where query and hit lengths were not being output for fullblast.
→ Version 2.18.0: Added blaste filtering to be applied to existing BLAST results.
→ Version 2.19.0: Added maxall=X limits to all-by-all analyses. Added qassemble=T.
→ Version 2.19.1: Fixed handling of basefile and results generation for blastres=FILE.
→ Version 2.19.2: Modified output to be in rank order.

• gopher: Updated from Version 3.4.
→ Version 3.4.1: Fixed stripXGap issue. (Why was this being implemented anyway?). Added REST output.

• haqesac: Updated from Version 1.10.
→ Version 1.10.1: Tweaked QryVar interactivity.
→ Version 1.10.2: Corrected typos and disabled buggy post-HAQESAC data reduction.

• multihaq: Updated from Version 1.2.
→ Version 1.2.1: Updated documentation to include the HAQESAC reference.
→ Version 1.2.2: Switched default to keepblast=T. Added forking blasta=X command to BLAST.

• peptcluster: Updated from Version 1.4.
→ Version 1.5.0: Added peptalign=T/F/X function for aligning peptides using regex or minimal gap addition. Added REST.
→ Version 1.5.1: Updated REST output. Removed peptide redundancy.

• pingu_V4: Updated from Version 4.3.
→ Version 4.4.0: Converted ppicompile=T to ppicompile=LIST.
→ Version 4.5.0: Added hublist=LIST : List of hub genes to restrict pairwise PPI to, and pairwise parsing.

• qslimfinder: Updated from Version 2.0.
→ Version 2.1.0: Added PTMData and PTMList options.

• seqsuite: Updated from Version 1.4.0.
→ Version 1.5.0: Added extatic.ExTATIC and revert.REVERT. NOTE: Dev only.
→ Version 1.5.1: Added 'seq' as alias for 'rje_seq' - want to avoid rje_ prefix requirements.
→ Version 1.6.0: Added mitab and rje_mitab for MITAB parsing.
→ Version 1.6.1: Added extra error messages.
→ Version 1.7.0: Added pingu_V4.PINGU.
→ Version 1.8.0: Added rje_pacbio.PacBio.

• slimbench: Updated from Version 2.8.0.
→ Version 2.8.1: Removed use of Protein name for ELM Uniprot entries due to problems mapping old IDs.
→ Version 2.9.0: Added SLiMMaker ELM reduction table and output.
→ Version 2.9.1: Enabled download only with generate=F benchmark=F.
→ Version 2.10.0: Add generation of table mapping PPIBench dataset generation.

• slimfarmer: Updated from Version 1.4.1.
→ Version 1.4.2: Fixed log transfer issues due to new #VIO line. Better handling of crashed runs.

• slimfinder: Updated from Version 5.1.
→ Version 5.1.1: Modified alphabet handling and fixed musthave bug.
→ Version 5.2.0: Added PTMList and PTMData modes (dev only).

• slimmaker: Updated from Version 1.2.0.
→ Version 1.3.0: Added varlength option to identify gaps in aligned peptides and generate variable length motif.
→ Version 1.3.1: Fixed varlength option to work with end of peptide gaps. (Gaps ignored completely - should not be there!)
→ Version 1.4.0: Add iteration REST output.
→ Version 1.4.1: Add unmatched peptides REST output.
→ Version 1.4.2: Fixed bug with variable length wildcards at start of sequence.
→ Version 1.5.0: Added peptalign=X functionality, using PeptCluster peptide alignment.
→ Version 1.6.0: Added equiv=LIST : List (or file) of TEIRESIAS-style ambiguities to use [AGS,ILMVF,FYW,FYH,KRH,DE,ST]
→ Version 1.6.1: Fixed peptide case bug.

• slimparser: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.
→ Version 0.0.1: Fixed RestKeys bug.
→ Version 0.1.0: Added retrieval and parsing of existing server job. Added password.
→ Version 0.2.0: Added API access to REST server if restin is REST call (i.e. starts with http:)
→ Version 0.2.1: Added PureAPI output of API REST call returned text.
→ Version 0.3.0: Added parsing of input files to give to rest calls.
→ Version 0.3.1: Fixed issue that had broken REST server full output.

• slimprob: Updated from Version 2.2.0.
→ Version 2.2.1: Updated REST output.
→ Version 2.2.2: Modified input to allow motif=X in addition to motifs=X.
→ Version 2.2.3: Tweaked basefile setting and citation.

• slimsuite: Updated from Version 1.3.0.
→ Version 1.4.0: Added RLC and Disorder progs to call SLiMCore. Added CompariMotif.
→ Version 1.5.0: Added peptcluster and peptalign calls.

Updates in extras/:

• file_monster: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 1.0: Initial Working version
→ Version 1.1: Broadened away from strict extension-based scavenging to whole file names with wildcards
→ Version 1.2: Added DirSum function and updated FileMonster slightly.
→ Version 1.3: Added redundant file cleanup
→ Version 1.4: Added skiplist and purgelist
→ Version 1.5: Added rename function (to replace rename.pl Perl module)
→ Version 1.6: Minor bug fix.
→ Version 2.0: Major reworking with new object making use of rje_db tables etc. Old functions to be ported with time.
→ Version 2.1: Added dirsum function.
→ Version 2.2: Added fixendings=FILELIST to convert Mac \\r into UNIX \\n

• prodigis: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added probability calculations based on hydrophobicity, serine and cysteine.
→ Version 0.2: Added cysteine count and cysteine weighting.

• rje_glossary: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 1.0: Working version, including text setup for webserver.
→ Version 1.1: Added href=T option to add external hyperlinks for and [text] in descriptions [True]
→ Version 1.2: Added recognition of _italics_ markup.
→ Version 1.3: Fixed minor italicising bug.
→ Version 1.4: Added keeporder=T/F to maintain input order (e.g. for MapTime).

• rje_itunes: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added Plays/Track, default Album Artist and topHTML() method.

• rje_phos: Created/Renamed/moved.
→ Version 0.0: Initial Compilation. Basic pELM parsing done.
→ Version 0.1: Added phosBLAST method.

• rje_pydocs: Updated from Version 2.14.0.
→ Version 2.15.0: Added parsing and generation of "pages" for new rest server docs functions.
→ Version 2.15.1: Tweaked formatting of outfmt and docstring documentation.
→ Version 2.15.2: Tweaked formatting of docstring documentation.
→ Version 2.15.3: Fixed URL formatting of docstring documentation.
→ Version 2.16.0: Added Webserver tab to doc parsing from settings/*.form.
→ Version 2.16.1: Added parsing of imports within a try/except block. (Cannot be on same line as try: or except:)
→ Version 2.16.2: Tweaked makePages() output.

• rje_seqplot: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.

• rje_ssds: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.

• rje_yeast: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.

• wormpump: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.

Updates in libraries/:

• rje: Updated from Version 4.13.1.
→ Version 4.13.2: Removed excess REST HTML methods.
→ Version 4.13.3: Added uselower=False to dataDict() method.
→ Version 4.13.4: Added maxrep=X to listCombos() method.
→ Version 4.14.0: Added listToDict() method.
→ Version 4.15.1: Fixed matchExp method to be able to handline multilines. (Shame re.DOTALL doesn't work!)

• rje_blast_V2: Updated from Version 2.7.
→ Version 2.7.1: Added capacity to keep alignments following GABLAM calculations.
→ Version 2.7.2: Fixed bug with hitToSeq fasta output for rje_seqlist.SeqList objects.
→ Version 2.8.0: A more significant BLAST e-value setting will filter read results.
→ Version 2.9.0: Added qassemble=T/F : Whether to fully assemble query stats from all hits [False].
→ Version 2.9.1: Updated default BLAST and BLAST+ paths to '' for added modules.

• rje_db: Updated from Version 1.7.1.
→ Version 1.7.2: Fixed numerical join issue during Table.compress().
→ Version 1.7.3: Added lower case enforcement of headers for reading tables from file.
→ Version 1.7.4: Added optional restricted Field set for output.
→ Version 1.7.5: Added more error messages and tableNames() method.

• rje_ensembl: Updated from Version 2.14.
→ Version 2.15.0: Added capacity to download/process a section of Ensembl with speclist=LIST.
→ Version 2.15.1: Improved error handling for too many FTP connections: still need to fix problem!
→ Version 2.15.2: Trying to improve speed of Uniprot parsing for EnsLoci.

• rje_genbank: Updated from Version 1.2.2.
→ Version 1.3.0: Added split viral output.
→ Version 1.3.1: Fixed bug in split viral output.

• rje_html: Updated from Version 0.1.
→ Version 0.2.0: Added delimited text to HTML table conversion.
→ Version 0.2.1: Updated default CSS to http://www.slimsuite.unsw.edu.au/stylesheets/slimhtml.css.

• rje_mitab: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.
→ Version 0.1.0: Added complex=LIST : Complex identifier prefixes to expand from mapped PPI [complex]
→ Version 0.1.1: Fixed Evidence/IType parsing bug for BioGrid/Intact.
→ Version 0.2.0: Added splicevar=T/F option.

• rje_obj: Updated from Version 2.1.0.
→ Version 2.1.1: Removed excess REST HTML methods.
→ Version 2.1.2: Tweaked glist cmdRead warnings.

• rje_qsub: Updated from Version 1.6.1.
→ Version 1.6.2: Updated module list: blast+/2.2.30,clustalw,clustalo,fsa,mafft,muscle,pagan,R/3.1.1

• rje_scoring: Updated from Version -.

• rje_seq: Updated from Version 3.21.0.
→ Version 3.22.0: Added loading sequences from provided sequence files contents directly, bypassing file reading.
→ Version 3.22.1: Fixed problem if seqin is blank, triggering odd Uniprot download.
→ Version 3.23.0: Add speclist to reformat options.

• rje_seqlist: Updated from Version 1.10.0.
→ Version 1.11.0: Added more dna2prot reformatting options.

• rje_slim: Updated from Version 1.9.
→ Version 1.10.0: Added varlength option to makeSlim() method.
→ Version 1.10.1: Fixed varlength and terminal position compatibility.
→ Version 1.10.2: Fixed issue of [] returns.
→ Version 1.10.3: Fixed makeSlim bug with variable length wildcards at start of sequence.
→ Version 1.11.0: Added splitMotif() function.
→ Version 1.12.0: Added equiv to makeSlim() function.

• rje_slimcore: Updated from Version 2.6.1.
→ Version 2.7.0: Updating MegaSLiM function to work with REST server. Allow megaslim=seqin. Added iuscoredir=PATH and protscores=T/F.
→ Version 2.7.1: Modified iuscoredir=PATH and protscores=T/F to work without megaslim. Fixed UPC/SLiMdb issue for GOPHER.
→ Version 2.7.2: Fixed iuscoredir=PATH to stop raising errors when file not previously made.
→ Version 2.7.3: Fixed serverend message error.

• rje_slimhtml: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 0.3: Added code for making Random Dataset pages
→ Version 0.4: Updated UPC pages and added additional front pages.
→ Version 0.5: Split front page into front and full. Added GO tabs/pages.
→ Version 0.6: Added XGMML output.
→ Version 0.7: Modified output for HumSF10 and HAPPI analysis.
→ Version 0.8: Added SVG output. Integrated better with HAPPI code.
→ Version 0.9: Added SLiM Descriptions.

• rje_slimlist: Updated from Version 1.6.
→ Version 1.7.0: Added direct feeding of motif file content for loading (for REST servers).
→ Version 1.7.1: Modified input to allow motif=X in additon to motifs=X.
→ Version 1.7.2: Fixed bug that could not accept variable length motifs from commandline. Improved error message.

• rje_specificity: Updated from Version -.

• rje_tree: Updated from Version 2.11.0.
→ Version 2.11.1: Tweaked QryVar interactivity.
→ Version 2.11.2: Updated tree paths.

• rje_tree_group: Updated from Version -.

• rje_uniprot: Updated from Version 3.20.3.
→ Version 3.20.4: Fixed bug introduced by REST access modifications.
→ Version 3.20.5: Improved handling of downloads for uniprot IDs that have been updated (i.e. no direct mapping).
→ Version 3.20.6: Improved handling of zero accession numbers for extraction.
→ Version 3.20.7: Fixed uniformat default error.
→ Version 3.21.0: Added uparse=LIST option to try and accelerate parsing of large datasets for limited information.
→ Version 3.21.1: FullText is no longer stored in Uniprot object. Will need special handling if required.
→ Version 3.21.2: Fixed single uniprot extraction bug.
→ Version 3.21.3: Added REST datout to proteomes extraction.

• rje_xref: Updated from Version 1.3.0.
→ Version 1.3.1: Fixed xref list bug.
→ Version 1.4.0: Added optional Mapping dictionary for speeding up recurring mapping (should avoid if memsaver=F).
→ Version 1.5.0: Added stripvar=CDICT removal of variants using Field:Char list, e.g. Uniprot:-,GenPept:. []
→ Version 1.6.0: Added mapxref=LIST List of identifiers to map to KeyIDs using mapfields []

• rje_zen: Updated from Version 1.3.0.
→ Version 1.3.1: Added some more words.

Advanced Access - QSLiMFinder: improved short linear motif prediction using specific query protein data

QSLiMFinder paper now out. See Edwards Lab: Advanced Access - QSLiMFinder: improved short linear motif prediction using specific query protein data for more details.

Palopoli N, Lythgow KT & Edwards RJ (in press). QSLiMFinder: improved short linear motif prediction using specific query protein data. Bioinformatics 2015; doi: 10.1093/bioinformatics/btv155 [PDF]

SLiMSuite release 2015-01-07 now available

A new download of SLiMSuite (release 2015-01-07) is now available at both UK (U. Southampton) and Australia (UNSW) sites (svn r613).

Many of the changes are under the hood, in preparation for a new set of REST services, which will be coming soon. The new download also features two new programs in the tools/ folder, which will hopefully simplify running many of the programs. The core programs and several of the key accessory programs (e.g. rje_seq and rje_uniprot) can now be run using the main SLiMSuite program:

python tool/slimsuite.py -prog X

where X is one of the SLiMSuite or SeqSuite programs. To see which are currently supported, run with -help. Simply add additional commandline options for the chosen program (and/or use ini files) as normal. For program-specific help, run with help=T: this will give the help documentation for program X rather than SLiMSuite. (NB. SLiMSuite can be used to access both SLiMSuite and SeqSuite programs. There is also a seqsuite.py that can be used to access just the SeqSuite programs and accessories.)

The other major update is that SLiMSuite programs (SLiMProb, SLiMFinder, QSLiMFinder and SLiMCore) can now take lists of Uniprot accession numbers as alternative input, using uniprotid=LIST in place of seqin=FILE. Providing there is an open internet connection, the relevant proteins will be downloaded from the Uniprot server for analysis.

GABLAM has also benefited from the addition of a new fullblast=T mode, which will perform the full all versus all BLAST+ search prior to GABLAM processing. Depending on your machine setup, this can be faster than the current method that forks out a single sequence at a time and is more IO-intensive as a result. The GABLAM functions to use existing BLAST+ results have also been fixed and tidied a little. (If re-running might be required, keepblast=T can retain the full BLAST results file to accelerate subsequent runs.)

Updates since last release:

• fiesta: Updated from Version 1.8.
→ Version 1.8.1: Replaced type with stype throughout to try and avoid TypeError crashes.
→ Version 1.9.0: Altered HAQDB to be a list of files rather than just one.

• gablam: Updated from Version 2.14.
→ Version 2.15.0: Added seqnr function. Add run() method.
→ Version 2.16.0: Added fullblast=T/F : Whether to perform full BLAST followed by blastres analysis [False]
→ Version 2.16.1: Fixed a bug where the fullblast option was failing to return scores and evalues.

• multihaq: Updated from Version 1.1.
→ Version 1.2: Changed defaults to autoskip=F.

• pingu_V4: Updated from Version 4.2.
→ Version 4.3: Modified to use Pfam as hub field for DomPPI generation. Modified naming of PPI output after ppisource.

• seqsuite: Created/Renamed.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added rje_seq and FIESTA. Added Uniprot.
→ Version 1.0: Moved to tools/ for general release. Added HAQESAC and MultiHAQ. Moved mod to enable easy external access.
→ Version 1.1: Added XRef = rje_xref.XRef. Identifier cross-referencing module.
→ Version 1.2: Added taxonomy.
→ Version 1.3.0: Added rje_zen.Zen. Modified code to work with REST services.
→ Version 1.4.0: Added rje_tree.Tree, GABLAM and GOPHER.

• slimbench: Updated from Version 2.5.
→ Version 2.6: Added ELM domain interactions table: http://www.elm.eu.org/infos/browse_elm_interactiondomains.tsv.
→ Version 2.6: Fixed issues introduced with new SLiMCore V2.0 SLiMSuite code.
→ Version 2.7: Reinstate filtering. (Not sure why disabled.) Add genspec=LIST to filter by species. Added domlink=T/F.
→ Version 2.8.0: Implemented PPIBench benchmarking for datasets without Motifs in name.

• slimfarmer: Updated from Version 1.3.
→ Version 1.4: Added modules=LIST : List of modules to add in job file [clustalo,mafft]
→ Version 1.4.1: Fixed farm=batch mode for qsub=T.

• slimmaker: Updated from Version 1.1.
→ Version 1.2.0: Modified to work with REST servers

• slimmutant: Updated from Version 1.0.
→ Version 1.1: Minor tweaks to generate method to increase speed. (Make index in method.) Added splitfield=X.
→ Version 1.2: Added a batch mode for mutfiles - all other options will be kept fixed. Added maxmutant and minmutant.
→ Version 1.3: Added SLiMPPI analysis (will set analyse=T). Started basing on SLiMCore

• slimprob: Updated from Version 2.1.
→ Version 2.2.0: Added basic REST functionality.

• slimsuite: Created/Renamed.
→ Version 0.0: Initial Compilation based on SeqSuite.
→ Version 1.0: Moved to tools/ for general release. Added reading and using of SeqSuite programs.
→ Version 1.1: Added slimlist.
→ Version 1.2: Added SLiMBench.
→ Version 1.3.0: Added SLiMMaker and modified code to work with REST services.

• rje: Updated from Version 4.12.
→ Version 4.13.0: Added new built-in attributes/options for REST services.
→ Version 4.13.1: Fixed MemSaver typo in WarnLog output. Modified mkDir() to avoid clashes raising errors.

• rje_db: Updated from Version 1.5.
→ Version 1.6: Added option to save a subset of entries using saveToFile(savekeys=LIST).
→ Version 1.7.0: Added splitchar to table splitting.
→ Version 1.7.1: Reinstated raise error if expected table missing.

• rje_dismatrix_V3: Created/Renamed.
→ Version 3.0: Updated to new rje_obj.RJE_Object class.

• rje_ensembl: Updated from Version 2.13.
→ Version 2.14: Add enspep=T/F : Create full gnspacc EnsEMBL peptide datasets [False]

• rje_genbank: Added to download.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Modified and Tidied output a little.
→ Version 0.2: Added details to skip and option to use different detail for protein accession number.
→ Version 0.3: Added reloading of features.
→ Version 1.0: Basic functioning version. Added fetchuid=LIST Genbank retrieval to generate seqin=FILE.
→ Version 1.1: Added use of rje_taxonomy for getting Species Code from TaxID.
→ Version 1.2: Modified to deal with genbank protein entries.
→ Version 1.2.1: Fixed feature bug that was breaking parser and removing trailing '*' from protein sequences.
→ Version 1.2.2: Fixed more features that were breaking parser.

• rje_obj: Updated from Version 2.0.
→ Version 2.1.0: Added new built-in attributes/options for REST services.

• rje_ppi: Updated from Version 2.8.
→ Version 2.8.1: Fixed bug with Spring Layout interruption message.

• rje_qsub: Updated from Version 1.5.
→ Version 1.6: Added modules=LIST : List of modules to add in job file [clustalo,mafft]
→ Version 1.6.1: Added R/3.1.1 to modules.

• rje_seq: Updated from Version 3.20.
→ Version 3.21.0: Added extraction of uniprot IDs for seqin.

• rje_seqlist: Updated from Version 1.7.
→ Version 1.8: Added sortseq=X : Whether to sort sequences prior to output (size/invsize/accnum/name/seq/species/desc) [None]
→ Version 1.9.0: Added extra functions for returning sequence AccNum, ID or Species code.
→ Version 1.10.0: Added extraction of uniprot IDs for seqin. Added more dna2prot reformatting options.

• rje_sequence: Updated from Version 2.3.
→ Version 2.4: Added recognition of modified IPI format. Added standalone low complexity masking.
→ Version 2.4.1: Moved the gnspacc fragment recognition to reduce issues. Should perhaps remove completely?

• rje_slim: Updated from Version 1.8.
→ Version 1.9: Reinstated ambcut for slimToPattern()

• rje_slimcalc: Updated from Version 0.8.
→ Version 0.9: Improvements to use of GOPHER.

• rje_slimcore: Updated from Version 2.2.
→ Version 2.3: Docstring edits. Minor tweak to walltime() to close open files.
→ Version 2.4: Added megaslimfix=T/F : Whether to run megaslim in "fix" mode to tidy/repair existing files [False]
→ Version 2.5: Added (hidden) slimmutant=T/F : Whether to ignore '.p.\D\d+\D' at end of accnum. Made default append=True.
→ Version 2.6.0: Added uniprotid=LIST : Extract IDs/AccNums in list from Uniprot into BASEFILE.dat and use as seqin=FILE. []
→ Version 2.6.1: Removed the maxseq default setting.

• rje_slimlist: Updated from Version 1.4.
→ Version 1.5: Added run() method for slimsuite.py compatibility. Improved split motif handling.
→ Version 1.6: Modified to read in new ELM class download file with extra header information. Added varlength=T/F filter.
→ Version 1.6: Modified so that filtering one element of a split motif removes all.

• rje_tree: Updated from Version 2.10.
→ Version 2.11.0: Modified for standalone running as part of SeqSuite.

• rje_uniprot: Updated from Version 3.19.
→ Version 3.20: Updated dbsplit=T output and checked function with Pfam. Probably needs work for other databases.
→ Version 3.20.1: Added uniprotid=LIST as an alias to acclist=LIST and extract=LIST.
→ Version 3.20.2: Added extra sequence return methods to UniprotEntry. Added fasta REST output.
→ Version 3.20.3: Fixed bug if new uniprot extraction method fails.

• rje_xml: Created/Renamed.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added xml.sax functions.
→ Version 0.2: Added parsing from URL.

• rje_xref: Updated from Version 1.1.
→ Version 1.2: Added join=LIST Run in join mode for list of FILE:key1|...|keyN:JoinField [] and naturaljoin=T/F.
→ Version 1.3.0: Added compress=LIST to handle 1:many input data. []

• rje_zen: Updated from Version 1.2.
→ Version 1.3.0: Modified output to work with new REST service calls.