SLiMSuite 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.

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

Full Changelog: v1.9.1...v1.11.0

SLiMSuite v1.9.1 (2020-12-27)

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.

SLiMSuite v1.8.1 (2019-05-27)

This update has fast-forwarded the SLiMSuite release to v1.8.1 to be consistent with the tools/slimsuite.py wrapper script. A top level SLiMSuite.py file can now be run to access the main tools and functions of the package.

SLiMSuite REST servers have been updated to match this release.

A summary of the changes since the last release is given below.

NOTE: A minor bug fix in rje_disorder.py has been updated in the *.tgz file.

SLiMSuite updates

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.

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.

•...

SLiMSuite v1.4.0 (2018-07-02)

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 v1.3.0 (2017-12-18)

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...

SLiMSuite v1.2.0 (2016-09-12)

Long-overdue September 2016 release of SLiMSuite 2016-09-12 - v1.2.0. 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...

SLiMSuite v1.1.0 (2015-11-30)

November 2015 release of SLiMSuite 2015-11-30 - v1.1.0. 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 v1.0.0 (2015-07-06)

This release is a minor update of 2015-06-01 and was created primarily for generating a DOI through Zenodo for the upcoming SLiMScape publication. This release has been designated v1.0.0 but this version numbering should not be confused with the version numbering of the main slimsuite.py module itself.

Future releases through GitHub/Zenodo will increment the v.X.X.X version number.

SLiMSuite.2015-06-01

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.

Updates since previous release

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_...