Module: SeqSuite Description: Genomics and biological sequence analysis toolkit Version: 1.27.0 Last Edit: 10/12/21

Copyright © 2014 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_obj rje_zen rje_dbase rje_ensembl rje_genbank rje_gff rje_mitab rje_paf rje_ppi rje_pydocs rje_seq rje_seqlist rje_taxonomy rje_tree rje_uniprot rje_xref rje_blast_V2 buscomp fiesta gablam gasp gopher haqesac multihaq seqmapper pingu_V4 pagsat smrtscape snapper snp_mapper rje_samtools rje_apollo revert saaga diploidocus synbad samphaser depthkopy depthsizer extatic rje_genomics

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

SeqSuite is designed to be a front end for the expanding range of miscellaneous sequence utilities that are found within the SLiMSuite libraries/ modules. The relevant tool is given by the first system command, or selected using prog=X (or program=X). As much as possible, SeqSuite will emulate running that tool from the commandline, adding any matching X.ini file to the default commandline options read in (*before* settings read from seqsuite.ini itself). By default, the SeqList tool will be called (libraries/rje_seqlist.py) and read in commands from seqlist.ini.

Help for the selected tool can be accessed using the help=T option. Note that -h, -help or help alone will trigger the SeqSuite help (this!). As -help or help will also set help=T, these commands will trigger both the SeqSuite help and the selected program help (unless over-ruled by help=F). An explicit help=T command will only trigger the selected program help.

SeqSuite tools

The list of tools recognised by prog=X will be added here as the relevant code is added:
- Apollo = rje_apollo.Apollo GABLAM wrapper for searching against apollo genomes.
- BLAST = rje_blast_V2.BLASTRun. BLAST+ Control Module.
- BUSCOMP = buscomp.BUSCOMP. BUSCO Compiler and Comparison tool.
- DBase = rje_dbase.DatabaseController. Database downloading and processing.
- DepthKopy = depthkopy.DepthKopy. Single-copy read-depth based copy number analysis.
- DepthSizer = depthsizer.DepthSizer. Read-depth based genome size prediction.
- Diploidocus = diploidocus.Diploidocus. Diploid genome assembly analysis toolkit.
- Ensembl = rje_ensembl.EnsEMBL. EnsEMBL Processing/Manipulation.
- ExTATIC = extatic.ExTATIC. !!! Development only. Not available in main download. !!!
- FIESTA = fiesta.FIESTA. Fasta Input EST Analysis. Transcriptome annotation/querying.
- GABLAM = gablam.GABLAM. Global Analysis of BLAST Local AlignMents
- GASP = gasp.GASP. Gapped Ancestral Sequence Prediction.
- Genbank = rje_genbank.GenBank. Genbank fetching/parsing module.
- GFF = rje_gff.GFF. GFF File Parser and Manipulator.
- GOPHER = gopher.GOPHER. Generation of Orthologous Proteins from Homology-based Estimation of Relationships.
- HAQESAC = haqesac.HAQESAC. Homologue Alignment Quality, Establishment of Subfamilies and Ancestor Construction.
- MITAB = rje_mitab.MITAB. MITAB PPI parser.
- MultiHAQ = multihaq.MultiHAQ. Multi-Query HAQESAC controller.
- PAF = rje_paf.PAF. Minimap2 PAF to GABLAM format converter.
- PAFScaff = pafsaff.PAFScaff. Pairwise mApping Format reference-based scaffold anchoring and super-scaffolding.
- PAGSAT = pagsat.PAGSAT. Pairwise Assembled Genome Sequence Analysis Tool. (Development only)
- PINGU = pingu_V4.PINGU. Protein Interaction Network & GO Utility.
- PPI = rje_ppi.PPI. Protein-Protein Interaction Module.
- PyDocs = rje_pydocs.PyDoc. Python Module Documentation & Distribution.
- RJE_Seq = rje_seq.SeqList. Fasta file sequence manipulation/reformatting.
- SAAGA = saaga.SAAGA. Summarise, Annotate & Assess Genome Annotations
- SAMPhaser = samphaser.SAMPhaser. Diploid chromosome phasing from SAMTools Pileup format.
- SAMTools = rje_samtools.SAMTools. SAMTools mpileup analysis tool. (Development only)
- SeqList = rje_seqlist.SeqList. Fasta file sequence manipulation/reformatting.
- SeqMapper = seqmapper.SeqMapper. Sequence Mapping Program.
- SMRTSCAPE (/PacBio) = smrtscape.SMRTSCAPE. SMRT Subread Coverage & Assembly Parameter Estimator. (Development only)
- Snapper = snp_mapper.SNPMap. SNV to feature annotations mapping and rating tool. (Development only)
- Taxonomy = rje_taxonomy.Taxonomy. Taxonomy download/conversion tool.
- Tree = rje_tree.Tree. Phylogenetic Tree Module.
- Uniprot = rje_uniprot.Uniprot. Uniprot download and parsing module.
- XRef = rje_xref.XRef. Identifier cross-referencing module.
- Zen - rje_zen.Zen. Random Zen wisdom generator and test code.

Special run modes

- summarise = run seqlist summarise on each file in batchrun=FILELIST

Commandline

prog=X # Identifies the tool to be used. Will load defaults from X.ini (before seqsuite.ini) [seqlist]
help=T/F # Show the help documentation for program X. [False]

batchrun=FILELIST # Batch run the program on selected files (wildcards allowed) []
batcharg=X # Commandline argument to use for batchrun files ['seqin']
batchlog=X # Generate separate basefile.X log files for each batch run file (None for single log) [log]
batchbase=T/F # Whether to give each batch run a separate basefile=X command in place of log=X [True]

See also rje.py generic commandline options.

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Added rje_seq and FIESTA. Added Uniprot.
    # 1.0 - Moved to tools/ for general release. Added HAQESAC and MultiHAQ. Moved mod to enable easy external access.
    # 1.1 - Added XRef = rje_xref.XRef. Identifier cross-referencing module.
    # 1.2 - Added taxonomy.
    # 1.3.0 - Added rje_zen.Zen. Modified code to work with REST services.
    # 1.4.0 - Added rje_tree.Tree, GABLAM and GOPHER.
    # 1.5.0 - Added extatic.ExTATIC and revert.REVERT. NOTE: Dev only.
    # 1.5.1 - Added 'seq' as alias for 'rje_seq' - want to avoid rje_ prefix requirements.
    # 1.6.0 - Added mitab and rje_mitab for MITAB parsing.
    # 1.6.1 - Added extra error messages.
    # 1.7.0 - Added pingu_V4.PINGU.
    # 1.8.0 - Added rje_pacbio.PacBio.
    # 1.9.0 - Added PAGSAT and SMRTSCAPE.
    # 1.9.1 - Fixed HAQESAC setobjects=True error.
    # 1.10.0 - Added batchrun=FILELIST batcharg=X batch running mode.
    # 1.11.0 - Added SAMTools and Snapper/SNP_Mapper.
    # 1.11.1 - Redirected PacBio to call SMRTSCAPE.
    # 1.11.2 - Fixed batchrun batchlog=False log error.
    # 1.12.0 - Added Snapper.
    # 1.12.1 - Fixed possible download run bug. (No dev/ modules?)
    # 1.13.0 - Changed GABLAM defaults to fullblast=T keepblast=T.
    # 1.14.0 - Added BLAST run object, particularly for qassemblefas running.
    # 1.14.1 - Added zentest for testing the REST servers.
    # 1.15.0 - Added GASP to REST servers.
    # 1.16.0 - Add rje_gff.GFF to REST servers.
    # 1.17.0 - Added batch summarise mode.
    # 1.18.0 - Added rje_apollo.Apollo to REST servers.
    # 1.19.0 - Tweaked the output of batch summarise, adding Gap% and reducing dp for some fields.
    # 1.19.1 - Fixed GapPC summarise output to be a percentage, not a fraction.
    # 1.20.0 - Added rje_paf.PAF.
    # 1.21.0 - Added NG50 and LG50 to batch summarise.
    # 1.22.0 - Added BUSCOMP to programs.
    # 1.23.0 - Added rje_ppi.PPI to programs.
    # 1.23.1 - Fixed GCPC bug in summarise().
    # 1.23.2 - Dropped pacbio as synonym for smrtscape. (Causing REST server issues.)
    # 1.24.0 - Added SAAGA, Diploidocus, SynBad and rje_genomics to programs.
    # 1.25.0 - Added SeqMapper and SAMPhaser.
    # 1.26.0 - Added DepthSizer. Added gzip support to batch summarise.
    # 1.27.0 - Added DepthKopy.