diff GEMBASSY-1.0.3/doc/text/gshuffleseq.txt @ 0:8300eb051bea draft

Initial upload

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+++ b/GEMBASSY-1.0.3/doc/text/gshuffleseq.txt	Fri Jun 26 05:19:29 2015 -0400
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+                                  gshuffleseq
+Function
+
+   Create randomized sequence with conserved k-mer composition
+
+Description
+
+   gshuffleseq shuffles and randomizes the given sequence, conserving the
+   nucleotide/peptide k-mer content of the original sequence.
+
+   For k=1, i.e. shuffling sequencing preserving single nucleotide composition,
+   Fisher-Yates Algorithm is employed.
+   For k>1, shuffling preserves all k-mers (all k where k=1~k). For example,
+   k=3 preserves all triplet, doublet, and single nucleotide composition.
+   Algorithm for k-mer preserved shuffling is non-trivial, which is solved
+   by graph theoretical approach with Eulerian random walks in the graph of
+   k-1-mers. See Jiang et al., Kandel et al., and Propp et al., for details
+   of this algorithm.
+    
+   G-language SOAP service is provided by the
+   Institute for Advanced Biosciences, Keio University.
+   The original web service is located at the following URL:
+
+   http://www.g-language.org/wiki/soap
+
+   WSDL(RPC/Encoded) file is located at:
+
+   http://soap.g-language.org/g-language.wsdl
+
+   Documentation on G-language Genome Analysis Environment methods are
+   provided at the Document Center
+
+   http://ws.g-language.org/gdoc/
+
+Usage
+
+Here is a sample session with gshuffleseq
+
+% gshuffleseq tsw:hbb_human
+Create randomized sequence with conserved k-mer composition
+output sequence [hbb_human.fasta]: 
+
+   Go to the input files for this example
+   Go to the output files for this example
+
+Command line arguments
+
+   Standard (Mandatory) qualifiers:
+  [-sequence]          seqall     Sequence(s) filename and optional format, or
+                                  reference (input USA)
+  [-outseq]            seqout     [<sequence>.<format>] Sequence filename and
+                                  optional format (output USA)
+
+   Additional (Optional) qualifiers: (none)
+   Advanced (Unprompted) qualifiers:
+   -k                  integer    [1] Sequence k-mer to preserve composition
+                                  (Any integer value)
+
+   Associated qualifiers:
+
+   "-sequence" associated qualifiers
+   -sbegin1            integer    Start of each sequence to be used
+   -send1              integer    End of each sequence to be used
+   -sreverse1          boolean    Reverse (if DNA)
+   -sask1              boolean    Ask for begin/end/reverse
+   -snucleotide1       boolean    Sequence is nucleotide
+   -sprotein1          boolean    Sequence is protein
+   -slower1            boolean    Make lower case
+   -supper1            boolean    Make upper case
+   -scircular1         boolean    Sequence is circular
+   -sformat1           string     Input sequence format
+   -iquery1            string     Input query fields or ID list
+   -ioffset1           integer    Input start position offset
+   -sdbname1           string     Database name
+   -sid1               string     Entryname
+   -ufo1               string     UFO features
+   -fformat1           string     Features format
+   -fopenfile1         string     Features file name
+
+   "-outseq" associated qualifiers
+   -osformat2          string     Output seq format
+   -osextension2       string     File name extension
+   -osname2            string     Base file name
+   -osdirectory2       string     Output directory
+   -osdbname2          string     Database name to add
+   -ossingle2          boolean    Separate file for each entry
+   -oufo2              string     UFO features
+   -offormat2          string     Features format
+   -ofname2            string     Features file name
+   -ofdirectory2       string     Output directory
+
+   General qualifiers:
+   -auto               boolean    Turn off prompts
+   -stdout             boolean    Write first file to standard output
+   -filter             boolean    Read first file from standard input, write
+                                  first file to standard output
+   -options            boolean    Prompt for standard and additional values
+   -debug              boolean    Write debug output to program.dbg
+   -verbose            boolean    Report some/full command line options
+   -help               boolean    Report command line options and exit. More
+                                  information on associated and general
+                                  qualifiers can be found with -help -verbose
+   -warning            boolean    Report warnings
+   -error              boolean    Report errors
+   -fatal              boolean    Report fatal errors
+   -die                boolean    Report dying program messages
+   -version            boolean    Report version number and exit
+
+Input file format
+
+   The database definitions for following commands are available at
+   http://soap.g-language.org/kbws/embossrc
+
+   gshuffleseq reads one or more nucleotide or protein sequences.
+
+Output file format
+
+   The output from gshuffleseq is to .
+
+   File: hbb_human.fasta
+
+>HBB_HUMAN P68871 Hemoglobin subunit beta (Beta-globin) (Hemoglobin beta chain) (LVV-hemorphin-7)
+KGWLDLVAGAAHFVRRLKMLLEVDWAAHEERVGTSNPNNALKNEAADVEVHSPTHVNPTQ
+LVLVQVGFGTLHLQGVECPKPKPGGVALKPVAHLLAMKECTLVALGSDFYVDHGSDGEDK
+GFKAYVLATSFFAYTNFLHGKVKHVLF
+
+
+Data files
+
+   None.
+
+Notes
+
+   None.
+
+References
+
+   Fisher R.A. and Yates F. (1938) "Example 12", Statistical Tables, London
+
+   Durstenfeld R. (1964) "Algorithm 235: Random permutation", CACM 7(7):420
+
+   Jiang M., Anderson J., Gillespie J., and Mayne M. (2008) "uShuffle: 
+      a useful tool for shuffling biological sequences while preserving the
+      k-let counts", BMC Bioinformatics 9:192
+
+   Kandel D., Matias Y., Unver R., and Winker P. (1996) "Shuffling biological 
+      sequences", Discrete Applied Mathematics 71(1-3):171-185  
+
+   Propp J.G. and Wilson D.B. (1998) "How to get a perfectly random sample 
+      from a generic Markov chain and generate a random spanning tree of a 
+      directed graph", Journal of Algorithms 27(2):170-217
+
+   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
+      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
+      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
+
+   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
+      large-scale analysis of high-throughput omics data, J. Pest Sci.,
+      31, 7.
+
+   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
+      Analysis Environment with REST and SOAP Web Service Interfaces,
+      Nucleic Acids Res., 38, W700-W705.
+
+Warnings
+
+   None.
+
+Diagnostic Error Messages
+
+   None.
+
+Exit status
+
+   It always exits with a status of 0.
+
+Known bugs
+
+   None.
+
+See also
+
+   shuffleseq Shuffles a set of sequences maintaining composition
+
+Author(s)
+
+   Hidetoshi Itaya ([e-mail])
+   Institute for Advanced Biosciences, Keio University
+   252-0882 Japan
+
+   Kazuharu Arakawa ([e-mail])
+   Institute for Advanced Biosciences, Keio University
+   252-0882 Japan
+
+History
+
+   2012 - Written by Hidetoshi Itaya
+   2013 - Fixed by Hidetoshi Itaya
+
+Target users
+
+   This program is intended to be used by everyone and everything, from
+   naive users to embedded scripts.
+
+Comments
+
+   None.
+