getorf.ihelp

来自「emboss的linux版本的源代码」· IHELP 代码 · 共 119 行

   Standard (Mandatory) qualifiers:
  [-sequence]          seqall     Nucleotide sequence(s) filename and optional
                                  format, or reference (input USA)
  [-outseq]            seqoutall  [<sequence>.<format>] Protein sequence
                                  set(s) filename and optional format (output
                                  USA)

   Additional (Optional) qualifiers:
   -table              menu       [0] Code to use (Values: 0 (Standard); 1
                                  (Standard (with alternative initiation
                                  codons)); 2 (Vertebrate Mitochondrial); 3
                                  (Yeast Mitochondrial); 4 (Mold, Protozoan,
                                  Coelenterate Mitochondrial and
                                  Mycoplasma/Spiroplasma); 5 (Invertebrate
                                  Mitochondrial); 6 (Ciliate Macronuclear and
                                  Dasycladacean); 9 (Echinoderm
                                  Mitochondrial); 10 (Euplotid Nuclear); 11
                                  (Bacterial); 12 (Alternative Yeast Nuclear);
                                  13 (Ascidian Mitochondrial); 14 (Flatworm
                                  Mitochondrial); 15 (Blepharisma
                                  Macronuclear); 16 (Chlorophycean
                                  Mitochondrial); 21 (Trematode
                                  Mitochondrial); 22 (Scenedesmus obliquus);
                                  23 (Thraustochytrium Mitochondrial))
   -minsize            integer    [30] Minimum nucleotide size of ORF to
                                  report (Any integer value)
   -maxsize            integer    [1000000] Maximum nucleotide size of ORF to
                                  report (Any integer value)
   -find               menu       [0] This is a small menu of possible output
                                  options. The first four options are to
                                  select either the protein translation or the
                                  original nucleic acid sequence of the open
                                  reading frame. There are two possible
                                  definitions of an open reading frame: it can
                                  either be a region that is free of STOP
                                  codons or a region that begins with a START
                                  codon and ends with a STOP codon. The last
                                  three options are probably only of interest
                                  to people who wish to investigate the
                                  statistical properties of the regions around
                                  potential START or STOP codons. The last
                                  option assumes that ORF lengths are
                                  calculated between two STOP codons. (Values:
                                  0 (Translation of regions between STOP
                                  codons); 1 (Translation of regions between
                                  START and STOP codons); 2 (Nucleic sequences
                                  between STOP codons); 3 (Nucleic sequences
                                  between START and STOP codons); 4
                                  (Nucleotides flanking START codons); 5
                                  (Nucleotides flanking initial STOP codons);
                                  6 (Nucleotides flanking ending STOP codons))

   Advanced (Unprompted) qualifiers:
   -[no]methionine     boolean    [Y] START codons at the beginning of protein
                                  products will usually code for Methionine,
                                  despite what the codon will code for when it
                                  is internal to a protein. This qualifier
                                  sets all such START codons to code for
                                  Methionine by default.
   -circular           boolean    [N] Is the sequence circular
   -[no]reverse        boolean    [Y] Set this to be false if you do not wish
                                  to find ORFs in the reverse complement of
                                  the sequence.
   -flanking           integer    [100] If you have chosen one of the options
                                  of the type of sequence to find that gives
                                  the flanking sequence around a STOP or START
                                  codon, this allows you to set the number of
                                  nucleotides either side of that codon to
                                  output. If the region of flanking
                                  nucleotides crosses the start or end of the
                                  sequence, no output is given for this codon.
                                  (Any integer value)

   Associated qualifiers:

   "-sequence" associated qualifiers
   -sbegin1            integer    Start of each sequence to be used
   -send1              integer    End of each sequence to be used
   -sreverse1          boolean    Reverse (if DNA)
   -sask1              boolean    Ask for begin/end/reverse
   -snucleotide1       boolean    Sequence is nucleotide
   -sprotein1          boolean    Sequence is protein
   -slower1            boolean    Make lower case
   -supper1            boolean    Make upper case
   -sformat1           string     Input sequence format
   -sdbname1           string     Database name
   -sid1               string     Entryname
   -ufo1               string     UFO features
   -fformat1           string     Features format
   -fopenfile1         string     Features file name

   "-outseq" associated qualifiers
   -osformat2          string     Output seq format
   -osextension2       string     File name extension
   -osname2            string     Base file name
   -osdirectory2       string     Output directory
   -osdbname2          string     Database name to add
   -ossingle2          boolean    Separate file for each entry
   -oufo2              string     UFO features
   -offormat2          string     Features format
   -ofname2            string     Features file name
   -ofdirectory2       string     Output directory

   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