codcopy

 

Function

Reads and writes a codon usage table

Description

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Algorithm

**************** EDIT HERE ****************

Usage

Here is a sample session with codcopy


% codcopy 
Reads and writes a codon usage table
Codon usage file: Eecoli.cut
Output codon usage file [eecoli.cut]: 

Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-infile]            codon      Codon usage table name
  [-outfile]           outcodon   (no help text) outcodon value

   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 output type

   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
[-infile]
(Parameter 1)
Codon usage table name Codon usage file in EMBOSS data path  
[-outfile]
(Parameter 2)
(no help text) outcodon value Codon usage file  
Additional (Optional) qualifiers Allowed values Default
(none)
Advanced (Unprompted) qualifiers Allowed values Default
(none)

Input file format

codcopy reads any normal sequence USAs.

Output file format

codcopy outputs a graph to the specified graphics device. outputs a report format file. The default format is ...

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

**************** EDIT HERE ****************

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

See also

Program nameDescription
biosedReplace or delete sequence sections
cutseqRemoves a specified section from a sequence
degapseqRemoves gap characters from sequences
descseqAlter the name or description of a sequence
entretReads and writes (returns) flatfile entries
extractfeatExtract features from a sequence
extractseqExtract regions from a sequence
listorWrite a list file of the logical OR of two sets of sequences
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
notseqExclude a set of sequences and write out the remaining ones
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
seqretReads and writes (returns) sequences
seqretsplitReads and writes (returns) sequences in individual files
skipseqReads and writes (returns) sequences, skipping first few
splitterSplit a sequence into (overlapping) smaller sequences
trimestTrim poly-A tails off EST sequences
trimseqTrim ambiguous bits off the ends of sequences
unionReads sequence fragments and builds one sequence
vectorstripStrips out DNA between a pair of vector sequences
yankReads a sequence range, appends the full USA to a list file

Author(s)

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History

Target users

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

Comments

None