
                                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:L48662
output sequence(s) [l48662.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]            seqoutall  [.] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers:
   -shuffle            integer    [1] Number of shuffles (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
   -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 dying program messages

Input file format

   shuffleseq reads one or more sequence USAs.

  Input files for usage example

   'tembl:L48662' is a sequence entry in the example nucleic acid
   database 'tembl'

  Database entry: tembl:L48662

ID   L48662; SV 1; linear; mRNA; STD; MUS; 366 BP.
XX
AC   L48662;
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; Euarchontoglires; Glires; Rodentia; Sciurognathi; Muroidea;
OC   Muridae; Murinae; Mus.
XX
RN   [1]
RP   1-366
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
DR   IMGT/LIGM; L48662; L48662.
XX
FH   Key             Location/Qualifiers
FH
FT   source          1..366
FT                   /organism="Mus musculus"
FT                   /strain="C3H/HeJ-lpr/lpr"
FT                   /mol_type="mRNA"
FT                   /cell_line="C3H/F2-11"
FT                   /cell_type="hybridoma"
FT                   /tissue_type="spleen"
FT                   /db_xref="taxon:10090"
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: l48662.fasta

>L48662 L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA anti
body heavy chain mRNA.
aggtttttatattacaagcatactaagagactcgcgatgatcgcacaattccaaatgtgc
tcatgggtgtagcaagaacctcaaataaaagggcaaccatgagggtaaagtctccgcatg
agcccctgggacgcgagagactttctcccgctagtgggtcgaacctgcagtgtcgataat
tggagttaaaatcgcagcatttacggccatgaattgtgtcgatanacgattcacgcaatc
gttaagatcaggttcattgggntcacaaaccgtaggccccccgttgcctgacgcgtaacg
ttcggatttccgtgacttcatctgactactctgtcacattcttacacgacaagctcaaca
agccgg
>L48662 L48662.1 Mus musculus (cell line C3H/F2-11) chromosome 12 anti-DNA anti
body heavy chain mRNA.
gtggatggtatccctaacccatgacttgcgattccattgactaataccgatttcgctatg
cgaataatactgcacaataagcgctgggggttggtttaaanttgcgatgtattatcaggt
gcatcatacgcgtgtcttcaatcgcaggagaatacaaactcagtcccaagcctaaggcgc
gtgagacttcattagggcaacggatactgctaactagttaaactcgcatgtaacaactca
cctgagcggtcgtacatgggcctctcttcccgaagggttgttcgaaaaaagcattgatac
aggccaggcaagcaccacgtgtcagcactacgatggccgttntcaaagtagctcatacag
cctcgc

   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
