A new download of SLiMSuite (release 2014-06-22) is now available.
As well as fixing the minor GOPHER output bug, a new Taxonomy processing module (rje_taxonomy) has been added. Although primarily designed for use with other SLiMSuite programs, this module has some standalone functionality for generating lists of Taxa IDs and species codes. (Details to follow.)
Output for the main SLiMSuite programs, SLiMFinder, SLiMProb and QSLiMFinder has also been consolidated and made more consistent for both re-running analyses and running analyses with multiple settings (consecutively) in the same directory. The use of GOPHER for generating alignments for conservation masking in these programs has also been improved to enable forking. (Details to follow.)
The final change of note is that SLiMMaker is now used to generate a consensus motif for each cloud returned by (Q)SLiMFinder. Note that (by default), these consensus motifs will not necessarily cover all occurrences in the cloud. (See SLiMMaker for more information.)
Other miscellaneous updates are listed below.
Updates since last release:
• gablam: Updated from Version 2.12.
→ Version 2.13: Fixed Protein vs DNA GABLAM. Modified sequence extraction to handle larger sequences. Add blastdir=PATH/.
• gopher: Updated from Version 3.3.
→ Version 3.4: Fixed FullRBH paralogue duplication issue.
• pingu_V4: Updated from Version 4.1.
→ Version 4.2: Bug fixes for use of PPISource to create PPI databases. Add HGNC to sourcedata (xrefdata=HGNC)
• qslimfinder: Updated from Version 1.7.
→ Version 1.8: Added cloudfix=T/F Restrict output to clouds with 1+ fixed motif (recommended) [False]. Consolidating output.
• slimbench: Updated from Version 2.2.
→ Version 2.2: Modified the FN/TN and ResNum calculations. No longer rate TP in random data as OT.
→ Version 2.3: Changed the default to queries=F. SearchINI bug fix. Added occbench generation.
• slimfarmer: Updated from Version 1.1.
→ Version 1.2: Implemented the slimsuite=T/F option and got SLiMFarmer qsub to work with GOPHER forking.
• slimfinder: Updated from Version 4.6.
→ Version 4.7: Added SLiMMaker generation to motif clouds. Added Q and Occ to Chance column.
• slimprob: Updated from Version 1.2.
→ Version 1.3: Consolidating output file naming for consistency across SLiMSuite. (SLiMBuild = Motif input)
• rje: Updated from Version 4.10.
→ Version 4.11: Enabled '\t#' comments in ini files. Modified getStrLC to return '' for 'none' by default. Added listMax().
→ Version 4.11: Added self.name() to basic object class.
• rje_blast: Reinstated for SLiMDisc legacy compatibility.
• rje_ensembl: Reinstated and updated.
→ Version 2.11: Added rje_taxonomy and makeuniprot=T/F. Removed metlist. Moved release and species data extraction.
→ Version 2.12: Changed chromspec to enable downloads of all species but also download toplevel files, not chromosomes.
• rje_hmm_V1: Reinstated.
• rje_hpc: Updated from Version 1.0.
→ Version 1.1: Disabled memory checking in Windows and OSX.
• rje_motif_V3: Updated from Version 3.0.
→ Version 3.1: Fixed minor code bugs.
• rje_obj: Updated from Version 1.6.
→ Version 1.7: Added self.name() to basic object class.
• rje_seq: Updated from Version 3.18.
→ Version 3.19: Fixed BLAST+ sequence extraction name truncation error.
• rje_seqlist: Updated from Version 1.4.
→ Version 1.5: Added sampler=N(,X) : Generate (X) file(s) sampling a random N sequences from input into seqout.N.X.fas [0]
→ Version 1.6: Modified currSeq() and nextSeq() slightly to fix index mode breakage. Look out for other programs breaking.
→ Version 1.6: Add sequence fragment extraction.
• rje_slim: Updated from Version 1.6.
→ Version 1.7: Fixed import slimFix(slim) error that was reporting slimProb()
• rje_slimcalc: Updated from Version 0.7.
→ Version 0.8: Made RLC the default.
• rje_slimcore: Updated from Version 1.14.
→ Version 1.15: Added pre-running GOPHER if no alndir and usegopher=T. Updated dataset() to use Input not Basefile.
• rje_taxonomy: Created/Renamed.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Initial working version with rje_ensembl.
→ Version 1.0: Fully functional version with modified viral species code creation.
• rje_uniprot: Updated from Version 3.18.
→ Version 3.19: Updated and consolidated dbxref table generation (formerly linkout) using rje_db. Changed acc_num to accnum.
