Wednesday, 21 August 2013

New Software Release

New releases of SLiMSuite and SeqSuite are now available. Please note that RJESuite has now been discontinued - for simplicity, all of the extra gubbins is now part of the SeqSuite release. SLiMSuite still represents a cut-down version that focuses on Short Linear Motif analysis tools.

There have been a number of updates since the last release, which will be the focus of future posts. The biggest change since the last release is the implementation of BLAST+ as the default in place of BLAST for most tools. The old BLAST can still be invoked using the oldblast=T switch. In addition to blastpath=PATH, a new blast+path=PATH parameter will need to be set.

Apart from some file organisation tweaks, the other major change is that CompariMotif now has a memsaver=T mode, which will process very large motif lists much quicker and avoid memory issues. The XGMML output is not (yet) available in this mode. For multi-processor CPUs and large searchdb motif lists, CompariMotif now also supported forking (forks=X).

Documentation is in the process of having an overhaul and is still lagging behind as a result. Please ask if anything is unclear and that section of documentation will be prioritised.

Updates since last release:

• aphid: Updated from Version 2.0.
→ Version 2.1: Reduced import commands.

• budapest: Updated from Version 2.1.
→ Version 2.2: Removed unrequired rje_dismatrix import.
→ Version 2.3: Updated to use rje_blast_V2. Needs further updates for BLAST+. Deleted obsolete OLDreadMascot() method.

• comparimotif_V3: Updated from Version 3.9.
→ Version 3.10: Added MemSaver option, which will read and process input motifs (not searchdb) one motif at a time.
→ Version 3.10: Added forking.

• fiesta: Updated from Version 1.5.
→ Version 1.6: Removed HAQESAC import (uses MultiHAQ).
→ Version 1.7: Updated to use rje_blast_V2. Needs work to make function with BLAST+.

• gablam: Updated from Version 2.10.
→ Version 2.11: Altered to use BLAST+ and rje_blast_V2.

• gasp: Updated from Version 1.3.
→ Version 1.4: Minor tweaks to imports.

• gfessa: Updated from Version 1.2.
→ Version 1.3: Tidied module imports.
→ Version 1.4: Switched to rje_blast_V2. More work needed for BLAST+.

• haqesac: Updated from Version 1.8.
→ Version 1.9: Added rje_blast_V2 implementation and BLAST+. Use oldblast=T for old BLAST.

• peptcluster: Updated from Version 1.3.
→ Version 1.4: Bug fixes for end of sequence characters and different length peptides.

• picsi: Updated from Version 1.0.
→ Version 1.1: Updated to blast_V2 and BLAST+.

• pingu: Updated from Version 3.8.
→ Version 3.9: Tidied imports.

• qslimfinder: Updated from Version 1.5.
→ Version 1.6: Removed excess module imports.

• slimbench: Updated from Version 1.8.
→ Version 1.9: Added memsaver option. Replaced SLiMSearch with SLiMProb. Altered default IO paths.
→ Version 1.9: Removed 3DID again: new ELM interaction_domains file has position-specific PPI details.
→ Version 2.0: Major overhaul of input options to standardise/clarify. Implemented auto-downloads and PPI datasets.

• slimprob: Updated from Version 1.0.
→ Version 1.1: Tidied import commands.

• slimsuite: Created.
→ Version 0.0: Initial Compilation with downloadelm function.

• rje_pydocs: Updated from Version 2.6.
→ Version 2.7: Added rje_ppi output for module links.
→ Version 2.8: Added parsing of commandline options from docstring and cmdRead calls.
→ Version 2.8: Added docsource=PATH : Input path for Python Module documentation (manuals etc.) ['../docs/']

• rje: Updated from Version 4.6.
→ Version 4.7: Added self.warn list and self.warnLog() functions to Log object. Modified i=-1 quitchoice to raise not quit.
→ Version 4.8: Added perc cmdtype = float that is multiplied by 100.0 if < 1.0. Removed server option from iniCmds().

• rje_ancseq: Updated from Version 1.2.
→ Version 1.3: Changed "biproblem" error handling in gaspProbs()

• rje_blast_V1: Updated from Version 1.14.
→ Version 1.15: Added OldBLAST/Legacy option to Object for compatibility with rje_blast_V2. (Always True!)

• rje_blast_V2: Updated from Version 2.1.
→ Version 2.2: Added gablamData() to return old-style GABLAM dictionary from table.
→ Version 2.3: Added blastCluster() method to return UPC clustering and GABLAM distance matrix from a file.
→ Version 2.4: Scrapped BLAST "Run" field to simplify code - keep a single run per BLASTRun object.

• rje_db: Updated from Version 1.0.
→ Version 1.1: Added sortedEntries() function.
→ Version 1.2: Added Table.hasField(field). Add openTable(), readEntry() and readSet() methods.

• rje_forker: Created.
→ Version 0.0: Initial Compilation.

• rje_iridis: Updated from Version 1.8.
→ Version 1.9: Added scanning of legacy folder - moving GOPHER_V2!

• rje_obj: Updated from Version 1.0.
→ Version 1.1: Added rje_zen import and self.zen() to call rje_zen.Zen().wisdom().
→ Version 1.2: Added warnLog functions.
→ Version 1.3: Added perc cmdtype = float that is multiplied by 100.0 if < 1.0. Also added cmdtype = date for YYYY-MM-DD.

• rje_ppi: Updated from Version 2.7.
→ Version 2.8: Tweaked Spring Layout. Stores original Hub and Spoke Field.

• rje_seq: Updated from Version 3.16.
→ Version 3.17: Updated to use BLAST+ and rje_blast_V2

• rje_sequence: Updated from Version 2.2.
→ Version 2.3: Added alternative keys for sequence (for UniProt splice variants). Added SpliceVar dict.

• rje_slimcore: Updated from Version 1.10.
→ Version 1.11: Tidied some of the module imports.
→ Version 1.12: Upgraded BLAST to BLAST+. Can use old BLAST with oldblast=T.

• rje_slimlist: Updated from Version 1.1.
→ Version 1.2: Added some extra functions for CompariMotif Memsaver mode

• rje_tree: Updated from Version 2.9.
→ Version 2.10: Added cleanup of *.r.csv file following R-based PNG generation.

• rje_uniprot: Updated from Version 3.13.
→ Version 3.14: Added direct retrieval of UniProt entries from URL, including full proteomes. Updated output file naming.
→ Version 3.14: Added dblist=LIST and dbsplit=T/F for additional DB link output control. Set unipath default to url.

• rje_xml: Updated from Version 0.1.
→ Version 0.2: Added parsing from URL.

• rje_xref: Updated from Version 0.0.
→ Version 1.0: Added xfrom and xto fields and xMap() function for mapping from one ID set to another.

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