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codcopy
Wiki
The master copies of EMBOSS documentation are available at
http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.
Please help by correcting and extending the Wiki pages.
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
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