Software Open Access

slimsuite/SLiMSuite: SLiMSuite v1.4.0 (2018-07-02)

Richard J Edwards

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.

<h1>SLiMSuite updates</h1>

<h2>Updates in extras/:</h2>


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


<h2>Updates in libraries/:</h2>


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

<p><b>• rje_db:</b> <i>Updated from Version 1.8.6.</i> <br>→ Version 1.9.0: Added comment output to saveToFile(). </p>

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

<p><b>• rje_gff:</b> <i>Created/Renamed/moved.</i> <br>→ Version 0.0.0: Initial Compilation. <br>→ Version 0.1.0: Basic functional version. </p>

<p><b>• rje_hpc:</b> <i>Updated from Version 1.1.</i> <br>→ Version 1.1.1: Added output of subjob command to log as run. </p>

<p><b>• rje_html:</b> <i>Updated from Version 0.2.1.</i> <br>→ Version 0.3.0: Added optional loading of javascript files and stupidtable.js?dev default. </p>

<p><b>• rje_qsub:</b> <i>Updated from Version 1.9.1.</i> <br>→ Version 1.9.2: Modified qsub() to return job ID. </p>

<p><b>• rje_samtools:</b> <i>Updated from Version 1.19.2.</i> <br>→ Version 1.20.0: Added parsing of BAM file - needs samtools on system. Added minsoftclip=X, maxsoftclip=X and minreadlen=X. </p>

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

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

<p><b>• rje_slimcalc:</b> <i>Updated from Version 0.9.3.</i> <br>→ Version 0.10.0: Added extra disorder methods to slimcalc. </p>

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

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

<p><b>• rje_uniprot:</b> <i>Updated from Version 3.24.1.</i> <br>→ Version 3.24.2: Updated HTTP to HTTPS. Having some download issues with server failures. <br>→ 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]. </p>

<p><b>• rje_zen:</b> <i>Updated from Version 1.3.2.</i> <br>→ Version 1.4.0: Added some more words and "They fight crime!" structure. </p>

<h2>Updates in tools/:</h2>


<p><b>• gablam:</b> <i>Updated from Version 2.28.3.</i> <br>→ Version 2.29.0: Added localGFF=T/F output </p>

<p><b>• gasp:</b> <i>Updated from Version 1.4.</i> <br>→ Version 2.0.0: Upgraded to rje_obj framework for REST server. </p>

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

<p><b>• gopher:</b> <i>Updated from Version 3.4.2.</i> <br>→ Version 3.4.3: Added checking and warning if no bootstraps for orthtree. </p>

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

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

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

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

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

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

<p><b>• slimfinder:</b> <i>Updated from Version 5.3.3.</i> <br>→ Version 5.3.4: Fixed terminal (^/$) musthave bug. </p>

<p><b>• slimsuite:</b> <i>Updated from Version 1.7.0.</i> <br>→ Version 1.7.1: Added error raising for protected REST alias data. </p>

<p><b>• smrtscape:</b> <i>Updated from Version 2.2.1.</i> <br>→ Version 2.2.2: Added dna=T to all SeqList object generation. </p>

<p><b>• snapper:</b> <i>Updated from Version 1.6.0.</i> <br>→ Version 1.6.1: Fixed bug for reducing to unique-unique pairings that was over-filtering. </p> <!-- ~~~~~~~~~~~~~~ HTML tail data ~~~~~~~~~~~~~~~~~ -->

<HR><FONT COLOR=#979E45 SIZE=2>© RJ Edwards 2018. Last modified 2 Jul 2018.</FONT></P>

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