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.