Monday 12 September 2016

SLiMSuite release v1.2.0 (2016-09-12) online

The long-overdue September 2016 release of SLiMSuite 2016-09-12 - v1.2.0 is now on GitHub. Apart from a few bug fixes, the main updates in this release are to the tools for PacBio genomics, notably PAGSAT, SMRTSCAPE and a new SNP Mapping tool, Snapper. These are still in development and need further documentation but are ready for use with a little help. Please get in touch if you are interested. Proper documentation and example use will hopefully follow soon, as the first PacBio yeast paper is written.

GABLAM has had some minor tweaks for improved function with Snapper, PAGSAT and another developmental tool that will be in the next release (REVERT - available via the REST servers). These have been focused on the fragfas=T output of fragmented BLAST hits based on local alignments. This includes addition of a new default to reverse complement reverse hits (fragrevcomp=T) and the separation of parameters for splitting up local hits into multiple fragments (gablamfrag=X) and merging close/overlapping fragments (fragmerge=X).

SLiMSuite updates in this release

Updates in extras/:

• rje_pydocs: Updated from Version 2.16.2.
→ Version 2.16.3: Fixed docstring REST parsing to work with _V* modules.

Updates in libraries/:

• rje: Updated from Version 4.15.1.
→ Version 4.16.0: Added list2dict(inlist,inkeys) and dict2list(indict,inkeys) functions.
→ Version 4.16.1: Improved handling of integer parameters when given bad commands.
→ Version 4.17.0: Added extra functions to randomList()

• rje_blast_V2: Updated from Version 2.9.1.
→ Version 2.10.0: Added nocoverage calculation based on local alignment table.
→ Version 2.11.0: Added localFragFas output method.
→ Version 2.11.1: Fixed snp local table revcomp bug. [Check this!]
→ Version 2.11.2: Fixed GABLAM calculation bug when '*' in protein sequences.

• rje_db: Updated from Version 1.8.0.
→ Version 1.8.1: Added sfdict to saveTable output.

• rje_genbank: Updated from Version 1.3.2.
→ Version 1.4.0: Added addtags=T/F : Add locus_tag identifiers if missing - needed for gene/cds/prot fasta output [False]
→ Version 1.4.1: Fixed genetic code warning.
→ Version 1.5.0: Added setupRefGenome() method based on PAGSAT code.
→ Version 1.5.1: Fixed logskip append locus sequence file bug.
→ Version 1.5.2: Fixed addtag(s) bug.

• rje_hprd: Updated from Version 1.2.
→ Version 1.2.1: Fixed "PROTEIN_ARCHITECTURE" bug.

• rje_menu: Updated from Version 0.3.
→ Version 0.4.0: Changed handling of default for exiting menu loop. May affect behaviour of some existing menus.

• rje_mitab: Updated from Version 0.2.0.
→ Version 0.2.1: Fixed redundant evidence/itype bug (primarily dip)

• rje_obj: Updated from Version 2.1.3.
→ Version 2.2.0: Added screenwrap=X.
→ Version 2.2.1: Improved handling of integer parameters when given bad commands.

• rje_samtools: Updated from Version 0.1.0.
→ Version 0.2.0: Added majmut=T/F : Whether to restrict output and stats to positions with non-reference Major Allele [False]
→ Version 1.0.0: Major reworking. Old version frozen as rje_samtools_V0.
→ Version 1.1.0: Added snptabmap=X,Y alternative SNPTable mapping and read_depth statistics []. Added majref=T/F.
→ Version 1.2.0: Added developmental combining of read mapping onto two different genomes.
→ Version 1.3.0: Major debugging and code clean up.
→ Version 1.4.0: Added parsing of read number (to link SNPs) and fixed deletion error at same time. Added rid=T/F and snponly=T/F.
→ Version 1.5.0: Added biallelic=T/F : Whether to restrict SNPs to pure biallelic SNPs (two alleles meeting mincut) [False]
→ Version 1.5.1: Fixed REF/Ref ALT/Alt bug.
→ Version 1.6.0: Added majfocus=T/F : Whether the focus is on Major Alleles (True) or Mutant/Reference Alleles (False) [True]
→ Version 1.7.0: Added parsing of *.sam files for generating RID table.
→ Version 1.8.0: Added read coverage summary/checks.
→ Version 1.8.1: Fixed issue when RID file not generated by pileup parsing. Set RID=True by default to avoid issues.

• rje_samtools_V0: Created/Renamed/moved.
→ Version 0.0: Initial Compilation.
→ Version 0.1.0: Modified version to handle multiple loci per file. (Original was for single bacterial chromosomes.)
→ Version 0.2.0: Added majmut=T/F : Whether to restrict output and stats to positions with non-reference Major Allele [False]

• rje_seq: Updated from Version 3.23.0.
→ Version 3.24.0: Added REST seqout output.

• rje_seqlist: Updated from Version 1.15.3.
→ Version 1.15.4: Fixed REST server output bug.
→ Version 1.15.5: Fixed reformat=fasta default issue introduced from fixing REST output bug.
→ Version 1.16.0: Added edit=T sequence edit mode upon loading (will switch seqmode=list).
→ Version 1.17.0: Added additional summarise=T output for seqmode=db.
→ Version 1.18.0: Added revcomp to reformat options.
→ Version 1.19.0: Added option log description for deleting sequence during edit.
→ Version 1.20.0: Added option to give a file of changes for edit mode.
→ Version 1.20.1: Fixed edit=FILE deletion bug.

• rje_sequence: Updated from Version 2.5.2.
→ Version 2.5.3: Fixed genetic code warning error.

• rje_slimcore: Updated from Version 2.7.5.
→ Version 2.7.6: Added feature masking log info or warning.
→ Version 2.7.7: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour.

• rje_synteny: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.

• rje_taxonomy: Updated from Version 1.1.0.
→ Version 1.2.0: Added storage of Parents.

• rje_tree: Updated from Version 2.13.0.
→ Version 2.14.0: Added cladeSpec().

• rje_uniprot: Updated from Version 3.21.4.
→ Version 3.22.0: Tweaked REST table output.

• rje_xref: Updated from Version 1.8.0.
→ Version 1.8.1: Added rest run mode to avoid XRef table output if no gene ID list is given. Added `genes` and `genelist` as `idlist=LIST` synonym.
→ Version 1.8.2: Catching self.dict['Mapping'] error for REST server.

• snp_mapper: Updated from Version 0.4.0.
→ Version 0.5.0: Added CDS rating.
→ Version 0.6.0: Added AltFT mapping mode (map features to AltLocus and AltPos)
→ Version 0.7.0: Added additional fields for processing Snapper output. (Hopefully will still work for SAMTools etc.)
→ Version 0.8.0: Added parsing of GFF file from Prokka.
→ Version 0.8.1: Corrected "intron" classification for first position of features. Updated FTBest defaults.
→ Version 1.0.0: Version that works with Snapper V1.0.0. Not really designed for standalone running any more.

Updates in tools/:

• comparimotif_V3: Updated from Version 3.12.
→ Version 3.13.0: Added REST server function.

• gablam: Updated from Version 2.20.0.
→ Version 2.21.0: Added nocoverage Table output of regions missing from pairwise SNP Table.
→ Version 2.21.1: Added fragrevcomp=T/F : Whether to reverse-complement DNA fragments that are on reverse strand to query [True]
→ Version 2.22.0: Added description to HitSum table.
→ Version 2.22.1: Added localaln=T/F to keep local alignment sequences in the BLAST local Table.
→ Version 2.22.2: Fixed local output error. (Query/Qry issue - need to fix this and make consistent!)
→ Version 2.22.3: Fixed blastv and blastb error: limit also applies to individual pairwise hits!
→ Version 2.23.0: Divided GablamFrag and FragMerge.

• pagsat: Updated from Version 1.6.1.
→ Version 1.7.0: Added tidy=T/F option. (Development)
→ Version 1.7.1: Updated tidy=T/F to include initial assembly.
→ Version 1.7.2: Fixed some bugs introduced by changing gablam fragment output.
→ Version 1.7.3: Added circularise sequence generation.
→ Version 1.8.0: Added orphan processing and non-chr naming of Reference.
→ Version 1.9.0: Modified the join sorting and merging. Added better tracking of positions when trimming.
→ Version 1.9.1: Added joinmargin=X : Number of extra bases allowed to still be considered an end local BLAST hit [10]
→ Version 1.10.0: Added weighted tree output and removed report warning.
→ Version 1.10.1: Fixed issue related to having Description in GABLAM HitSum tables.
→ Version 1.10.2: Tweaked haploid core output.
→ Version 1.10.3: Fixed tidy bug for RevComp contigs and switched joinsort default to Identity. (Needs testing.)
→ Version 1.10.4: Added genetar option to tidy out genesummary and protsummary output. Incorporated rje_synteny.
→ Version 1.10.5: Set gablamfrag=1 for gene/protein hits.
→ Version 1.11.0: Consolidated automated tidy mode and cleaned up some excess code.
→ Version 1.11.1: Added option for running self-PAGSAT of ctidX contigs versus haploid set. Replaced ctid "X" with "N".
→ Version 1.11.2: Fixed Snapper run choice bug.

• pingu_V4: Updated from Version 4.5.3.
→ Version 4.6.0: Added hubonly=T/F : Whether to restrict pairwise PPI to those with both hub and spoke in hublist [False]
→ Version 4.6.1: Fixed some ppifas=T/F bugs and added combineppi=T/F : Whether to combine all spokes into a single fasta file [False]
→ Version 4.6.2: Added check/filter for multiple SpokeUni pointing to same sequence. (Compilation redundancy mapping failure!)
→ Version 4.6.3: Fixed issue with 1:many SpokeUni:Spoke mappings messing up XHub.
→ Version 4.7.0: Added ppidbreport=T/F : Summary output for PPI compilation of evidence/PPIType/DB overlaps [True]
→ Version 4.8.0: Fixed report duplication issue and added additional summary output

• qslimfinder: Updated from Version 2.1.0.
→ Version 2.1.1: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour.

• seqsuite: Updated from Version 1.11.0.
→ Version 1.11.1: Redirected PacBio to call SMRTSCAPE.
→ Version 1.11.2: Fixed batchrun batchlog=False log error.
→ Version 1.12.0: Added Snapper.

• slimfarmer: Updated from Version 1.4.3.
→ Version 1.4.4: Modified default vmem request to 126GB from 127GB.
→ Version 1.4.5: Updated BLAST loading default to 2.2.31

• slimfinder: Updated from Version 5.2.1.
→ Version 5.2.2: Added warnings for ambocc and minocc that exceed the absolute minima. Updated docstring.
→ Version 5.2.3: Switched feature masking OFF by default to give consistent Uniprot versus FASTA behaviour. Fixed FTMask=T/F bug.

• slimparser: Updated from Version 0.3.3.
→ Version 0.3.4: Tweaked error messages.
→ Version 0.4.0: Added simple json format output.

• slimprob: Updated from Version 2.2.4.
→ Version 2.2.5: Fixed FTMask=T/F bug.

• slimsearch: Updated from Version 1.7.
→ Version 1.7.1: Minor modification to docstring. Preparation for update to SLiMSearch 2.0 optimised for proteome searches.

• slimsuite: Updated from Version 1.5.1.
→ Version 1.5.2: Updated XRef REST call.
→ Version 1.6.0: Removed SLiMCore as default. Default will now show help.

• smrtscape: Updated from Version 1.8.0.
→ Version 1.9.0: Updated empirical preassembly mapefficiency calculation.
→ Version 1.10.0: Added batch processing of subread files.
→ Version 1.10.1: Fixed bug in batch processing.

• snapper: Created/Renamed/moved.
→ Version 0.0.0: Initial Compilation.
→ Version 0.1.0: Tidied up with improved run pickup.
→ Version 0.2.0: Added FASTQ and improved CNV output along with all features.
→ Version 0.2.1: Fixed local output error. (Query/Qry issue - need to fix this and make consistent!) Fixed snp local table revcomp bug.
→ Version 0.2.2: Corrected excess CNV table output (accnum AND shortname).
→ Version 0.2.3: Corrected "intron" classification for first position of features. Updated FTBest defaults.
→ Version 1.0.0: Working version with completed draft manual. Added to SeqSuite.
→ Version 1.0.1: Fixed issues when features missing.