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codcopy
Function
Reads and writes a codon usage table
Description
Copies a codon usage table. This program supports all available codon
usage input and output formats. 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.
Algorithm
Usage
Here is a sample session with codcopy
% codcopy
Reads and writes 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
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 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
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
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
biosed Replace or delete sequence sections
cutseq Removes a specified section from a sequence
degapseq Removes gap characters from sequences
descseq Alter the name or description of a sequence
entret Reads and writes (returns) flatfile entries
extractalign Extract regions from a sequence alignment
extractfeat Extract features from a sequence
extractseq Extract regions from a sequence
listor Write a list file of the logical OR of two sets of sequences
makenucseq Creates random nucleotide sequences
makeprotseq Creates random protein sequences
maskfeat Mask off features of a sequence
maskseq Mask off regions of a sequence
newseq Type in a short new sequence
noreturn Removes carriage return from ASCII files
notseq Exclude a set of sequences and write out the remaining ones
nthseq Writes one sequence from a multiple set of sequences
pasteseq Insert one sequence into another
revseq Reverse and complement a sequence
seqret Reads and writes (returns) sequences
seqretsplit Reads and writes (returns) sequences in individual files
skipseq Reads and writes (returns) sequences, skipping first few
splitter Split a sequence into (overlapping) smaller sequences
trimest Trim poly-A tails off EST sequences
trimseq Trim ambiguous bits off the ends of sequences
union Reads sequence fragments and builds one sequence
vectorstrip Strips out DNA between a pair of vector sequences
yank Reads a sequence range, appends the full USA to a list file
Author(s)
Peter Rice (pmr ebi.ac.uk)
Informatics Division, 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
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