                                   codcopy



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Function

   Copy and reformat a codon usage table

Description

   codcopy reads and writes a codon usage table. Rather than a copy
   utility, it is intended as a format conversion utility so that codon
   usage data can be exported to other applications that support only a
   single format. This program supports all available codon usage input
   and output formats.

Usage

   Here is a sample session with codcopy


% codcopy
Copy and reformat a codon usage table
Codon usage file: Eecoli.cut
Codon usage output file [eecoli.cut]:


   Go to the output files for this example

Command line arguments

Copy and reformat a codon usage table
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-infile]            codon      Codon usage table name
  [-outfile]           outcodon   Codon usage table name

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-infile" associated qualifiers
   -format1            string     Data format

   "-outfile" associated qualifiers
   -odirectory2        string     Output directory
   -oformat2           string     Output format specific to this data type

   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

   codcopy reads a codon usage file.

Output file format

   codcopy writes a codon usage table. The user can choose any supported
   output format. ,p> See the full specification of codon tabel formats
   at:
   http://emboss.sourceforge.net/docs/themes/CodonUsage.html

  Output files for usage example

  File: eecoli.cut

#Species: Escherichia coli K12
#Division: gbbct
#Release: CUTG146
#CdsCount: 5045

#Coding GC 51.81%
#1st letter GC 58.93%
#2nd letter GC 40.69%
#3rd letter GC 55.80%

#Codon AA Fraction Frequency Number
GCA    A     0.214    20.299  32456
GCC    A     0.269    25.493  40761
GCG    A     0.355    33.631  53773
GCT    A     0.162    15.354  24549
TGC    C     0.554     6.431  10283
TGT    C     0.446     5.180   8282
GAC    D     0.372    19.047  30454
GAT    D     0.628    32.219  51514
GAA    E     0.690    39.570  63268
GAG    E     0.310    17.782  28431
TTC    F     0.425    16.580  26510
TTT    F     0.575    22.423  35852
GGA    G     0.108     7.925  12671
GGC    G     0.402    29.403  47013
GGG    G     0.150    10.994  17578
GGT    G     0.340    24.838  39714
CAC    H     0.429     9.712  15529
CAT    H     0.571    12.903  20630
ATA    I     0.072     4.290   6860
ATC    I     0.419    24.999  39971
ATT    I     0.510    30.427  48649
AAA    K     0.767    33.618  53752
AAG    K     0.233    10.198  16305
CTA    L     0.036     3.860   6172
CTC    L     0.104    11.045  17660
CTG    L     0.496    52.821  84455
CTT    L     0.104    11.051  17670
TTA    L     0.131    13.913  22246
TTG    L     0.129    13.727  21948
ATG    M     1.000    27.778  44414
AAC    N     0.551    21.611  34554
AAT    N     0.449    17.633  28193
CCA    P     0.192     8.524  13629
CCC    P     0.125     5.531   8843
CCG    P     0.524    23.235  37150
CCT    P     0.159     7.045  11265
CAA    Q     0.349    15.474  24742
CAG    Q     0.651    28.832  46100
AGA    R     0.037     2.056   3287
AGG    R     0.022     1.216   1944
CGA    R     0.064     3.542   5663
CGC    R     0.398    22.005  35184
CGG    R     0.098     5.391   8619
CGT    R     0.381    21.020  33609
AGC    S     0.277    16.031  25632
AGT    S     0.151     8.723  13947
TCA    S     0.123     7.137  11411
TCC    S     0.148     8.591  13736
TCG    S     0.154     8.916  14256
TCT    S     0.147     8.507  13601
ACA    T     0.131     7.035  11248
ACC    T     0.435    23.362  37354
ACG    T     0.268    14.371  22977
ACT    T     0.166     8.922  14265
GTA    V     0.154    10.883  17400
GTC    V     0.215    15.221  24336
GTG    V     0.371    26.253  41976
GTT    V     0.260    18.394  29410
TGG    W     1.000    15.303  24468
TAC    Y     0.429    12.243  19576
TAT    Y     0.571    16.326  26103
TAA    *     0.642     2.025   3237
TAG    *     0.072     0.228    365
TGA    *     0.286     0.902   1443

Data files

   None

Notes

   None.

References

   None.

Warnings

   None.

Diagnostic Error Messages

   None.

Exit status

   It always exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   aligncopy        Read and write alignments
   aligncopypair    Read and write pairs from alignments
   biosed           Replace or delete sequence sections
   cai              Calculate codon adaptation index
   chips            Calculate Nc codon usage statistic
   codcmp           Codon usage table comparison
   cusp             Create a codon usage table from nucleotide sequence(s)
   cutseq           Remove a section from a sequence
   degapseq         Remove non-alphabetic (e.g. gap) characters from sequences
   descseq          Alter the name or description of a sequence
   entret           Retrieve sequence entries from flatfile databases and files
   extractalign     Extract regions from a sequence alignment
   extractfeat      Extract features from sequence(s)
   extractseq       Extract regions from a sequence
   featcopy         Read and write a feature table
   featmerge        Merge two overlapping feature tables
   featreport       Read and write a feature table
   feattext         Return a feature table original text
   listor           Write a list file of the logical OR of two sets of sequences
   makenucseq       Create random nucleotide sequences
   makeprotseq      Create random protein sequences
   maskambignuc     Mask all ambiguity characters in nucleotide sequences with
                    N
   maskambigprot    Mask all ambiguity characters in protein sequences with X
   maskfeat         Write a sequence with masked features
   maskseq          Write a sequence with masked regions
   newseq           Create a sequence file from a typed-in sequence
   nohtml           Remove mark-up (e.g. HTML tags) from an ASCII text file
   noreturn         Remove carriage return from ASCII files
   nospace          Remove whitespace from an ASCII text file
   notab            Replace tabs with spaces in an ASCII text file
   notseq           Write to file a subset of an input stream of sequences
   nthseq           Write to file a single sequence from an input stream of
                    sequences
   nthseqset        Read and write (return) one set of sequences from many
   pasteseq         Insert one sequence into another
   revseq           Reverse and complement a nucleotide sequence
   seqcount         Read and count sequences
   seqret           Read and write (return) sequences
   seqretsetall     Read and write (return) many sets of sequences
   seqretsplit      Read sequences and write them to individual files
   sizeseq          Sort sequences by size
   skipredundant    Remove redundant sequences from an input set
   skipseq          Read and write (return) sequences, skipping first few
   splitsource      Split sequence(s) into original source sequences
   splitter         Split sequence(s) into smaller sequences
   syco             Draw synonymous codon usage statistic plot for a nucleotide
                    sequence
   trimest          Remove poly-A tails from nucleotide sequences
   trimseq          Remove unwanted characters from start and end of sequence(s)
   trimspace        Remove extra whitespace from an ASCII text file
   union            Concatenate multiple sequences into a single sequence
   vectorstrip      Remove vectors from the ends of nucleotide sequence(s)
   yank             Add a sequence reference (a full USA) to a list file

Author(s)

   Peter Rice
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

Target users

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

Comments

   None
