|
|
codcopy |
Please help by correcting and extending the Wiki pages.
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.
% 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
Copy and reformat a codon usage table
Version: EMBOSS:6.4.0.0
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
|
| 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 |
#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 |
| Program name | Description |
|---|---|
| aligncopy | Reads and writes alignments |
| aligncopypair | Reads and writes pairs from alignments |
| biosed | Replace or delete sequence sections |
| cai | Calculate codon adaptation index |
| chips | Calculates Nc codon usage statistic |
| codcmp | Codon usage table comparison |
| cusp | Create a codon usage table from nucleotide sequence(s) |
| 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 |
| 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 | 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 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 |
| seqcount | Reads and counts sequences |
| 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 |
| 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 | Removes vectors from the ends of nucleotide sequence(s) |
| yank | Add a sequence reference (a full USA) to a list file |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.