📄 codcopy.txt

📁 emboss的linux版本的源代码
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                                  codcopy Function   Reads and writes a codon usage tableDescription   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.AlgorithmUsage   Here is a sample session with codcopy% codcopy Reads and writes a codon usage tableCodon usage file: Eecoli.cutCodon usage output file [eecoli.cut]:    Go to the output files for this exampleCommand 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 messagesInput 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 NumberGCA    A     0.214    20.299  32456GCC    A     0.269    25.493  40761GCG    A     0.355    33.631  53773GCT    A     0.162    15.354  24549TGC    C     0.554     6.431  10283TGT    C     0.446     5.180   8282GAC    D     0.372    19.047  30454GAT    D     0.628    32.219  51514GAA    E     0.690    39.570  63268GAG    E     0.310    17.782  28431TTC    F     0.425    16.580  26510TTT    F     0.575    22.423  35852GGA    G     0.108     7.925  12671GGC    G     0.402    29.403  47013GGG    G     0.150    10.994  17578GGT    G     0.340    24.838  39714CAC    H     0.429     9.712  15529CAT    H     0.571    12.903  20630ATA    I     0.072     4.290   6860ATC    I     0.419    24.999  39971ATT    I     0.510    30.427  48649AAA    K     0.767    33.618  53752AAG    K     0.233    10.198  16305CTA    L     0.036     3.860   6172CTC    L     0.104    11.045  17660CTG    L     0.496    52.821  84455CTT    L     0.104    11.051  17670TTA    L     0.131    13.913  22246TTG    L     0.129    13.727  21948ATG    M     1.000    27.778  44414AAC    N     0.551    21.611  34554AAT    N     0.449    17.633  28193CCA    P     0.192     8.524  13629CCC    P     0.125     5.531   8843CCG    P     0.524    23.235  37150CCT    P     0.159     7.045  11265CAA    Q     0.349    15.474  24742CAG    Q     0.651    28.832  46100AGA    R     0.037     2.056   3287AGG    R     0.022     1.216   1944CGA    R     0.064     3.542   5663CGC    R     0.398    22.005  35184CGG    R     0.098     5.391   8619CGT    R     0.381    21.020  33609AGC    S     0.277    16.031  25632AGT    S     0.151     8.723  13947TCA    S     0.123     7.137  11411TCC    S     0.148     8.591  13736TCG    S     0.154     8.916  14256TCT    S     0.147     8.507  13601ACA    T     0.131     7.035  11248ACC    T     0.435    23.362  37354ACG    T     0.268    14.371  22977ACT    T     0.166     8.922  14265GTA    V     0.154    10.883  17400GTC    V     0.215    15.221  24336GTG    V     0.371    26.253  41976GTT    V     0.260    18.394  29410TGG    W     1.000    15.303  24468TAC    Y     0.429    12.243  19576TAT    Y     0.571    16.326  26103TAA    *     0.642     2.025   3237TAG    *     0.072     0.228    365TGA    *     0.286     0.902   1443Data files   NoneNotes   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 fileAuthor(s)   Peter Rice (pmr
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