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SeqSuite V1.12.1

Miscellaneous biological sequence analysis toolkit

Module: SeqSuite
Description: Miscellaneous biological sequence analysis toolkit
Version: 1.12.1
Last Edit: 13/09/16

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


Imported modules: rje rje_obj rje_zen rje_dbase rje_ensembl rje_genbank rje_mitab rje_pydocs rje_seq rje_seqlist rje_taxonomy rje_tree rje_uniprot rje_xref fiesta gablam gopher haqesac multihaq pingu_V4 pagsat smrtscape snapper snp_mapper rje_samtools revert extatic


See SLiMSuite Blog for further documentation.

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:
- DBase = rje_dbase.DatabaseController. Database downloading and processing.
- 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
- Genbank = rje_genbank.GenBank. Genbank fetching/parsing module.
- 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.
- PAGSAT = pagsat.PAGSAT. Pairwise Assembled Genome Sequence Analysis Tool. (Development only)
- PINGU = pingu_V4.PINGU. Protein Interaction Network & GO Utility.
- PyDocs = rje_pydocs.PyDoc. Python Module Documentation & Distribution.
- RJE_Seq = rje_seq.SeqList. Fasta file sequence manipulation/reformatting.
- SAMTools = rje_samtools.SAMTools. SAMTools mpileup analysis tool. (Development only)
- SeqList = rje_seqlist.SeqList. Fasta file sequence manipulation/reformatting.
- 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.

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?)

© 2015 RJ Edwards. Contact: richard.edwards@unsw.edu.au.