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.

Algorithm

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:6.2.0

   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

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-infile]
(Parameter 1)
codon Codon usage table name Codon usage file in EMBOSS data path  
[-outfile]
(Parameter 2)
outcodon Codon usage table name Codon usage file  
Additional (Optional) qualifiers
(none)
Advanced (Unprompted) qualifiers
(none)
Associated qualifiers
"-infile" associated codon qualifiers
-format1
-format_infile
string Data format Any string  
"-outfile" associated outcodon qualifiers
-odirectory2
-odirectory_outfile
string Output directory Any string  
-oformat2
-oformat_outfile
string Output format specific to this data type Any string  
General qualifiers
-auto boolean Turn off prompts Boolean value Yes/No N
-stdout boolean Write first file to standard output Boolean value Yes/No N
-filter boolean Read first file from standard input, write first file to standard output Boolean value Yes/No N
-options boolean Prompt for standard and additional values Boolean value Yes/No N
-debug boolean Write debug output to program.dbg Boolean value Yes/No N
-verbose boolean Report some/full command line options Boolean value Yes/No Y
-help boolean Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose Boolean value Yes/No N
-warning boolean Report warnings Boolean value Yes/No Y
-error boolean Report errors Boolean value Yes/No Y
-fatal boolean Report fatal errors Boolean value Yes/No Y
-die boolean Report dying program messages Boolean value Yes/No Y
-version boolean Report version number and exit Boolean value Yes/No N

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 Reads and writes alignments
aligncopypair Reads and writes pairs from alignments
biosed Replace or delete sequence sections
cutseq Removes a section from a sequence
degapseq Removes non-alphabetic (e.g. gap) characters from sequences
descseq Alter the name or description of a sequence
entret Retrieves 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 Reads and writes a feature table
featreport Reads and writes a feature table
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 Masks all ambiguity characters in nucleotide sequences with N
maskambigprot Masks 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 all 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 Reads and writes (returns) one set of sequences from many
pasteseq Insert one sequence into another
revseq Reverse and complement a nucleotide sequence
seqret Reads and writes (returns) sequences
seqretsetall Reads and writes (returns) many sets of sequences
seqretsplit Reads sequences and writes them to individual files
sizeseq Sort sequences by size
skipredundant Remove redundant sequences from an input set
skipseq Reads and writes (returns) sequences, skipping first few
splitsource Split sequence(s) into original source sequences
splitter Split sequence(s) into smaller sequences
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 Removes vectors from the ends of nucleotide sequence(s)
yank Add a sequence reference (a full USA) to a list file

Author(s)

Peter Rice (pmr © ebi.ac.uk)
European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Target users

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

Comments

None