Miscellaneous biological sequence analysis toolkit
Copyright © 2014 Richard J. Edwards - See source code for GNU License Notice
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
Help for the selected tool can be accessed using the
The list of tools recognised by
Special run modes
- summarise = run seqlist summarise on each file in
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.
© 2015 RJ Edwards. Contact: email@example.com.