Many of the changes are under the hood, in preparation for a new set of REST services, which will be coming soon. The new download also features two new programs in the
tools/ folder, which will hopefully simplify running many of the programs. The core programs and several of the key accessory programs (e.g.
rje_uniprot) can now be run using the main
python tool/slimsuite.py -prog X
X is one of the
SeqSuite programs. To see which are currently supported, run with
-help. Simply add additional commandline options for the chosen program (and/or use ini files) as normal. For program-specific help, run with
help=T: this will give the help documentation for program
X rather than
SLiMSuite can be used to access both
SeqSuite programs. There is also a
seqsuite.py that can be used to access just the
SeqSuite programs and accessories.)
The other major update is that
SLiMSuite programs (
SLiMCore) can now take lists of Uniprot accession numbers as alternative input, using
uniprotid=LIST in place of
seqin=FILE. Providing there is an open internet connection, the relevant proteins will be downloaded from the Uniprot server for analysis.
GABLAM has also benefited from the addition of a new
fullblast=T mode, which will perform the full all versus all BLAST+ search prior to GABLAM processing. Depending on your machine setup, this can be faster than the current method that forks out a single sequence at a time and is more IO-intensive as a result. The
GABLAM functions to use existing BLAST+ results have also been fixed and tidied a little. (If re-running might be required,
keepblast=T can retain the full BLAST results file to accelerate subsequent runs.)
Updates since last release:
• fiesta: Updated from Version 1.8.
→ Version 1.8.1: Replaced type with stype throughout to try and avoid TypeError crashes.
→ Version 1.9.0: Altered HAQDB to be a list of files rather than just one.
• gablam: Updated from Version 2.14.
→ Version 2.15.0: Added seqnr function. Add run() method.
→ Version 2.16.0: Added fullblast=T/F : Whether to perform full BLAST followed by blastres analysis [False]
→ Version 2.16.1: Fixed a bug where the fullblast option was failing to return scores and evalues.
• multihaq: Updated from Version 1.1.
→ Version 1.2: Changed defaults to autoskip=F.
• pingu_V4: Updated from Version 4.2.
→ Version 4.3: Modified to use Pfam as hub field for DomPPI generation. Modified naming of PPI output after ppisource.
• seqsuite: Created/Renamed.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added rje_seq and FIESTA. Added Uniprot.
→ Version 1.0: Moved to tools/ for general release. Added HAQESAC and MultiHAQ. Moved mod to enable easy external access.
→ Version 1.1: Added XRef = rje_xref.XRef. Identifier cross-referencing module.
→ Version 1.2: Added taxonomy.
→ Version 1.3.0: Added rje_zen.Zen. Modified code to work with REST services.
→ Version 1.4.0: Added rje_tree.Tree, GABLAM and GOPHER.
• slimbench: Updated from Version 2.5.
→ Version 2.6: Added ELM domain interactions table: http://www.elm.eu.org/infos/browse_elm_interactiondomains.tsv.
→ Version 2.6: Fixed issues introduced with new SLiMCore V2.0 SLiMSuite code.
→ Version 2.7: Reinstate filtering. (Not sure why disabled.) Add genspec=LIST to filter by species. Added domlink=T/F.
→ Version 2.8.0: Implemented PPIBench benchmarking for datasets without Motifs in name.
• slimfarmer: Updated from Version 1.3.
→ Version 1.4: Added modules=LIST : List of modules to add in job file [clustalo,mafft]
→ Version 1.4.1: Fixed farm=batch mode for qsub=T.
• slimmaker: Updated from Version 1.1.
→ Version 1.2.0: Modified to work with REST servers
• slimmutant: Updated from Version 1.0.
→ Version 1.1: Minor tweaks to generate method to increase speed. (Make index in method.) Added splitfield=X.
→ Version 1.2: Added a batch mode for mutfiles - all other options will be kept fixed. Added maxmutant and minmutant.
→ Version 1.3: Added SLiMPPI analysis (will set analyse=T). Started basing on SLiMCore
• slimprob: Updated from Version 2.1.
→ Version 2.2.0: Added basic REST functionality.
• slimsuite: Created/Renamed.
→ Version 0.0: Initial Compilation based on SeqSuite.
→ Version 1.0: Moved to tools/ for general release. Added reading and using of SeqSuite programs.
→ Version 1.1: Added slimlist.
→ Version 1.2: Added SLiMBench.
→ Version 1.3.0: Added SLiMMaker and modified code to work with REST services.
• rje: Updated from Version 4.12.
→ Version 4.13.0: Added new built-in attributes/options for REST services.
→ Version 4.13.1: Fixed MemSaver typo in WarnLog output. Modified mkDir() to avoid clashes raising errors.
• rje_db: Updated from Version 1.5.
→ Version 1.6: Added option to save a subset of entries using saveToFile(savekeys=LIST).
→ Version 1.7.0: Added splitchar to table splitting.
→ Version 1.7.1: Reinstated raise error if expected table missing.
• rje_dismatrix_V3: Created/Renamed.
→ Version 3.0: Updated to new rje_obj.RJE_Object class.
• rje_ensembl: Updated from Version 2.13.
→ Version 2.14: Add enspep=T/F : Create full gnspacc EnsEMBL peptide datasets [False]
• rje_genbank: Added to download.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Modified and Tidied output a little.
→ Version 0.2: Added details to skip and option to use different detail for protein accession number.
→ Version 0.3: Added reloading of features.
→ Version 1.0: Basic functioning version. Added fetchuid=LIST Genbank retrieval to generate seqin=FILE.
→ Version 1.1: Added use of rje_taxonomy for getting Species Code from TaxID.
→ Version 1.2: Modified to deal with genbank protein entries.
→ Version 1.2.1: Fixed feature bug that was breaking parser and removing trailing '*' from protein sequences.
→ Version 1.2.2: Fixed more features that were breaking parser.
• rje_obj: Updated from Version 2.0.
→ Version 2.1.0: Added new built-in attributes/options for REST services.
• rje_ppi: Updated from Version 2.8.
→ Version 2.8.1: Fixed bug with Spring Layout interruption message.
• rje_qsub: Updated from Version 1.5.
→ Version 1.6: Added modules=LIST : List of modules to add in job file [clustalo,mafft]
→ Version 1.6.1: Added R/3.1.1 to modules.
• rje_seq: Updated from Version 3.20.
→ Version 3.21.0: Added extraction of uniprot IDs for seqin.
• rje_seqlist: Updated from Version 1.7.
→ Version 1.8: Added sortseq=X : Whether to sort sequences prior to output (size/invsize/accnum/name/seq/species/desc) [None]
→ Version 1.9.0: Added extra functions for returning sequence AccNum, ID or Species code.
→ Version 1.10.0: Added extraction of uniprot IDs for seqin. Added more dna2prot reformatting options.
• rje_sequence: Updated from Version 2.3.
→ Version 2.4: Added recognition of modified IPI format. Added standalone low complexity masking.
→ Version 2.4.1: Moved the gnspacc fragment recognition to reduce issues. Should perhaps remove completely?
• rje_slim: Updated from Version 1.8.
→ Version 1.9: Reinstated ambcut for slimToPattern()
• rje_slimcalc: Updated from Version 0.8.
→ Version 0.9: Improvements to use of GOPHER.
• rje_slimcore: Updated from Version 2.2.
→ Version 2.3: Docstring edits. Minor tweak to walltime() to close open files.
→ Version 2.4: Added megaslimfix=T/F : Whether to run megaslim in "fix" mode to tidy/repair existing files [False]
→ Version 2.5: Added (hidden) slimmutant=T/F : Whether to ignore '.p.\D\d+\D' at end of accnum. Made default append=True.
→ Version 2.6.0: Added uniprotid=LIST : Extract IDs/AccNums in list from Uniprot into BASEFILE.dat and use as seqin=FILE. 
→ Version 2.6.1: Removed the maxseq default setting.
• rje_slimlist: Updated from Version 1.4.
→ Version 1.5: Added run() method for slimsuite.py compatibility. Improved split motif handling.
→ Version 1.6: Modified to read in new ELM class download file with extra header information. Added varlength=T/F filter.
→ Version 1.6: Modified so that filtering one element of a split motif removes all.
• rje_tree: Updated from Version 2.10.
→ Version 2.11.0: Modified for standalone running as part of SeqSuite.
• rje_uniprot: Updated from Version 3.19.
→ Version 3.20: Updated dbsplit=T output and checked function with Pfam. Probably needs work for other databases.
→ Version 3.20.1: Added uniprotid=LIST as an alias to acclist=LIST and extract=LIST.
→ Version 3.20.2: Added extra sequence return methods to UniprotEntry. Added fasta REST output.
→ Version 3.20.3: Fixed bug if new uniprot extraction method fails.
• rje_xml: Created/Renamed.
→ Version 0.0: Initial Compilation.
→ Version 0.1: Added xml.sax functions.
→ Version 0.2: Added parsing from URL.
• rje_xref: Updated from Version 1.1.
→ Version 1.2: Added join=LIST Run in join mode for list of FILE:key1|...|keyN:JoinField  and naturaljoin=T/F.
→ Version 1.3.0: Added compress=LIST to handle 1:many input data. 
• rje_zen: Updated from Version 1.2.
→ Version 1.3.0: Modified output to work with new REST service calls.