msbar.ihelp

来自「emboss的linux版本的源代码」· IHELP 代码 · 共 111 行

   Standard (Mandatory) qualifiers (* if not always prompted):
  [-sequence]          seqall     Sequence(s) filename and optional format, or
                                  reference (input USA)
   -count              integer    [1] Number of times to perform the mutation
                                  operations (Integer 0 or more)
   -point              menu       [0] Types of point mutations to perform
                                  (Values: 0 (None); 1 (Any of the following);
                                  2 (Insertions); 3 (Deletions); 4 (Changes);
                                  5 (Duplications); 6 (Moves))
   -block              menu       [0] Types of block mutations to perform
                                  (Values: 0 (None); 1 (Any of the following);
                                  2 (Insertions); 3 (Deletions); 4 (Changes);
                                  5 (Duplications); 6 (Moves))
*  -codon              menu       [0] Types of codon mutations to perform.
                                  These are only done if the sequence is
                                  nucleic. (Values: 0 (None); 1 (Any of the
                                  following); 2 (Insertions); 3 (Deletions); 4
                                  (Changes); 5 (Duplications); 6 (Moves))
  [-outseq]            seqoutall  [<sequence>.<format>] Sequence set(s)
                                  filename and optional format (output USA)

   Additional (Optional) qualifiers (* if not always prompted):
*  -inframe            boolean    [N] Do 'codon' and 'block' operations in
                                  frame

   Advanced (Unprompted) qualifiers:
   -othersequence      seqall     [asis:N] If you require that the resulting
                                  mutated sequence should not match a set of
                                  other sequences, then you can specify that
                                  set of sequences here. For example, if you
                                  require that the mutated sequence should not
                                  be the same as the input sequence, enter
                                  the input sequence here. If you want the
                                  result to be different to previous results
                                  of this program, specify the previous result
                                  sequences here. The program will check that
                                  the result does not match the sequences
                                  specified here before writing it out. If a
                                  match is found, then the mutation is started
                                  again with a fresh copy of the input
                                  sequence. If, after 10 such retries, there
                                  is still a match to the set of sequence
                                  given here, then the matching mutated
                                  sequence is written with a warning message.
   -minimum            integer    [1] Minimum size for a block mutation
                                  (Integer 0 or more)
   -maximum            integer    [10] Maximum size for a block mutation (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

   "-othersequence" associated qualifiers
   -sbegin             integer    Start of each sequence to be used
   -send               integer    End of each sequence to be used
   -sreverse           boolean    Reverse (if DNA)
   -sask               boolean    Ask for begin/end/reverse
   -snucleotide        boolean    Sequence is nucleotide
   -sprotein           boolean    Sequence is protein
   -slower             boolean    Make lower case
   -supper             boolean    Make upper case
   -sformat            string     Input sequence format
   -sdbname            string     Database name
   -sid                string     Entryname
   -ufo                string     UFO features
   -fformat            string     Features format
   -fopenfile          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