
                                shuffleseq 



Function

   Shuffles a set of sequences maintaining composition

Description

   This takes a sequence as input and outputs one or more sequences whose
   order has been randomly shuffled. No bases or residues are changed,
   only their order.

   The number of shuffled sequences output can be set by the '-shuffle'
   qualifier.

Usage

   Here is a sample session with shuffleseq

   This makes two randomised copies of the input sequence:


% shuffleseq -shuffle 2 
Shuffles a set of sequences maintaining composition
Input sequence(s): tembl:mmam
Output sequence [mmam.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 database USA
  [-outseq]            seqoutall  Output sequence(s) USA

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -shuffle            integer    Number of shuffles

   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
   -sformat1            string     Input sequence format
   -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 standard output
   -filter              boolean    Read standard input, write 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. 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 deaths


   Standard (Mandatory) qualifiers Allowed values Default
   [-sequence]
   (Parameter 1) Sequence database USA Readable sequence(s) Required
   [-outseq]
   (Parameter 2) Output sequence(s) USA Writeable sequence(s)
   <sequence>.format
   Additional (Optional) qualifiers Allowed values Default
   (none)
   Advanced (Unprompted) qualifiers Allowed values Default
   -shuffle Number of shuffles Any integer value 1

Input file format

   shuffleseq reads one or more sequence USAs.

  Input files for usage example

   'tembl:mmam' is a sequence entry in the example nucleic acid database
   'tembl'

  Database entry: tembl:mmam

ID   MMAM       standard; RNA; MUS; 366 BP.
XX
AC   L48662;
XX
SV   L48662.1
XX
DT   04-NOV-1995 (Rel. 45, Created)
DT   04-MAR-2000 (Rel. 63, Last updated, Version 4)
XX
DE   Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibody heavy
DE   chain mRNA.
XX
KW   .
XX
OS   Mus musculus (house mouse)
OC   Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia
;
OC   Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-366
RX   MEDLINE; 96409289.
RX   PUBMED; 8814271.
RA   Wloch M.K., Alexander A.L., Pippen A.M., Pisetsky D.S., Gilkeson G.S.;
RT   "Differences in V kappa gene utilization and VH CDR3 sequence among
RT   anti-DNA from C3H-lpr mice and lupus mice with nephritis";
RL   Eur. J. Immunol. 26(9):2225-2233(1996).
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..366
FT                   /db_xref="taxon:10090"
FT                   /organism="Mus musculus"
FT                   /strain="C3H/HeJ-lpr/lpr"
FT                   /cell_line="C3H/F2-11"
FT                   /cell_type="hybridoma"
FT                   /tissue_type="spleen"
XX
SQ   Sequence 366 BP; 100 A; 90 C; 85 G; 89 T; 2 other;
     gagnnccagc tgcagcagtc tggacctgag ctggtaaagc ctggggcttc agtgaagatg        6
0
     tcctgcaagg cttctggata cacattcact agctatgtta tgcactgggt gaatcagaag       12
0
     cctgggcagg gccttgagtg gattggatat attaatcctt acaatgatgg tactaactac       18
0
     aatgagaagt tcaaaggcaa ggccacactg acttcagaca aatcctccag cacagcctac       24
0
     atggagttca gcagcctgac ctctgaggac tctgcggtct attactgtgc aagaaaaact       30
0
     tcctactata gtaacctata ttactttgac tactggggcc aaggcaccac tctcacagtc       36
0
     tcctca                                                                  36
6
//

Output file format

  Output files for usage example

  File: mmam.fasta

>MMAM L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibo
dy heavy chain mRNA.
cgctactcatcggtgcctctgggtagcacctgggacctaggtgtgagagttcttgatgat
ccaccccagacggggtgtaattctctgtccccagacaccagcatagcggtgcctgcgtgc
accaattacgtttgacaaaccctaatattggcgagccgagcaantcaatcaaatgagcgg
gcgaacgagtcaaggaccgaacctccccaagatttattccaacgaattactattctcctt
tgtacgtatatatcttatatgcatcggtctatttgcgtcggatagcgtagtacaggcagt
cgaacctaccggcagtagtatgcaggagtnacaatgtcacatatcgagtattaagaacaa
agaata
>MMAM L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA antibo
dy heavy chain mRNA.
gaatttcaattctagatgaatccccaccgcccacaaaccgaccatcatcgacaaaacccc
gtctagtaggcttgtcagaggtaactttgcccaaacgcagcagaatgtgcgtgctgtaaa
gcacttattgccaccttngcccgcaaaaacccactcacaaaattccacgcggggtactca
ctagaatgtagtaggaagtcgatggttacgcgcgcacaacggccggtacagagattcggt
gggatctctaagtcagttgcgatttataacccggtaatttcaggatatagtcgttacggt
ggtgggtgaggcgcgttaagtttacccaagtnatcacgcgtttatagacgcttgcttaat
atgtta

   Each run will produce a different sequence.

   Note that these two sequences have the same name.

Data files

   None.

Notes

   This program may be useful for producing sets of sequences which can
   be used to check the statistics of sequence similarity finding
   software.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name              Description
   msbar        Mutate sequence beyond all recognition

Author(s)

   Michael Schmitz (mschmitz © lbl.gov)
   Lawrence Berkeley Labs, USA

History

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
