Software Open Access
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
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.
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.
• 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 
→ 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.