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$ ruff check --fix --select=I \ --config=lint.isort.force-single-line=true \ --config=lint.isort.order-by-type=false \ BioSQL/ Bio/ Tests/ Scripts/ Doc/ setup.py Using ruff version 0.4.10
Tue Aug 8 23:23:15 2000
Xbbtools
========
Xbbtools is a Graphical Sequence Editor originally written in Tcl/Tk with
BioWish. This is the start of a pure python re-implementation of xbbtools with
biopython.
Usage: xbbtools test.fas
What's available:
* open FASTA file
* display 1 or 6 frame translations ala DNA Strider
* all operations work on selection or complete sequence
* displays start, stop, length and composition of selection
* complement and reverse operations
* change genetic code
* very simple blast run menus
TODO:
* I'm waiting for a biopython modules for
- reading and writing different sequence formats
- spawning external programs/searches e.g. blast
without freezing the whole Tk mainloop
* implement biowish's ORF Displayer
* add Pyphy's database grabber tool
* speedup DNA seq operations suitable for complete genomes
* add windows support (shudder)
nextorf.py
==========
nextorf.py is a python re-implementation of the Tcl script nextorf.tcl
used together with xbbtools for ORF-fishing during the Complete Genome
Sequencing Project of the Typhus Bacteria Rickettsia Prowazekii developed
by Thomas Sicheritz-Ponten, Jan Andersson an Morten Andersen
Usage: nextorf.py testrp.fas
or nextorf.py -h
Feel free to suggest, fix and hack
... have fun
-thomas
Sicheritz Ponten Thomas E. CBS, Department of Biotechnology
blippblopp@linux.nu The Technical University of Denmark
CBS: +45 45 252485 Building 208, DK-2800 Lyngby
Fax +45 45 931585 http://www.cbs.dtu.dk/thomas/index.html
De Chelonian Mobile ... The Turtle Moves ...
Sicheritz-Ponten T.: BioWish: a molecular biology command extension to Tcl/Tk.
Comput Appl Biosci. 1997 Dec;13(6):621-2.
PMID: 9475992; UI: 98136469
Andersson SG, Zomorodipour A, Andersson JO, Sicheritz-Ponten T,
Alsmark UC, Podowski RM, Naslund AK, Eriksson AS, Winkler HH,
Kurland CG: The genome sequence of Rickettsia prowazekii and the origin of mitochondria.
Nature. 1998 Nov 12;396(6707):133-40.
PMID: 9823893; UI: 99039499