tfm.txt

emboss的linux版本的源代码

wordfinder       Match large sequences against one or more other sequences
wordmatch        Finds all exact matches of a given size between 2 sequences
wossname         Finds programs by keywords in their one-line documentation
yank             Reads a sequence range, appends the full USA to a list file


   Example 4

   Display only the groups that the programs can belong to:


% wossname -search '' -groups
Finds programs by keywords in their one-line documentation

ACD
ALIGNMENT CONSENSUS
ALIGNMENT DIFFERENCES
ALIGNMENT DOT PLOTS
ALIGNMENT GLOBAL
ALIGNMENT LOCAL
ALIGNMENT MULTIPLE
DISPLAY
EDIT
ENZYME KINETICS
FEATURE TABLES
HMM
INFORMATION
MENUS
NUCLEIC 2D STRUCTURE
NUCLEIC CODON USAGE
NUCLEIC COMPOSITION
NUCLEIC CPG ISLANDS
NUCLEIC GENE FINDING
NUCLEIC MOTIFS
NUCLEIC MUTATION
NUCLEIC PRIMERS
NUCLEIC PROFILES
NUCLEIC REPEATS
NUCLEIC RESTRICTION
NUCLEIC RNA FOLDING
NUCLEIC TRANSCRIPTION
NUCLEIC TRANSLATION
PHYLOGENY CONSENSUS
PHYLOGENY CONTINUOUS CHARACTERS
PHYLOGENY DISCRETE CHARACTERS
PHYLOGENY DISTANCE MATRIX
PHYLOGENY GENE FREQUENCIES
PHYLOGENY MOLECULAR SEQUENCE
PHYLOGENY TREE DRAWING
PROTEIN 2D STRUCTURE
PROTEIN 3D STRUCTURE
PROTEIN COMPOSITION
PROTEIN MOTIFS
PROTEIN MUTATION
PROTEIN PROFILES
TEST
UTILS DATABASE CREATION
UTILS DATABASE INDEXING
UTILS MISC

   Example 5

   Output html tags around the list of programs:


% wossname '' -html -out wossname.html
Finds programs by keywords in their one-line documentation

   Go to the output files for this example

Command line arguments

   Standard (Mandatory) qualifiers:
  [-search]            string     Enter a word or words here and a
                                  case-independent search for it will be made
                                  in the one-line documentation, group names
                                  and keywords of all of the EMBOSS programs.
                                  If no keyword is specified, all programs
                                  will be listed. (Any string is accepted)

   Additional (Optional) qualifiers:
   -explode            boolean    [N] The groups that EMBOSS applications
                                  belong to have two forms, exploded and not
                                  exploded. The exploded group names are more
                                  numerous and often vaguely phrased than the
                                  non-exploded ones. The exploded names are
                                  formed from definitions of the group names
                                  that start like NAME1:NAME2 and which are
                                  then expanded into many combinations of the
                                  names as: 'NAME1', 'NAME2', 'NAME1 NAME2',
                                  NAME2 NAME1'. The non-expanded names are
                                  simply like: 'NAME1 NAME2'.
   -[no]allmatch       boolean    [Y] By default, all words in the search
                                  string must match. This option searches for
                                  a match to any word in a list of
                                  possibilities
   -showkeywords       boolean    [N] Show keywords with program documentation
   -outfile            outfile    [stdout] Output file name
   -html               toggle     [N] If you are sending the output to a file,
                                  this will format it for displaying as a
                                  table in a WWW document.
   -groups             boolean    [N] If you use this option, then only the
                                  group names will output to the file
   -alphabetic         boolean    [N] If you use this option, then you will
                                  get a single list of the program names and
                                  descriptions instead of the programs being
                                  listed in their functional groups.

   Advanced (Unprompted) qualifiers:
   -[no]emboss         boolean    [Y] If you use this option then EMBOSS
                                  program documentation will be searched. If
                                  this option is set to be false, then only
                                  the EMBASSY programs will be searched (if
                                  the -embassy option is true). EMBASSY
                                  programs are not strictly part of EMBOSS,
                                  but use the same code libraries and share
                                  the same look and feel, but are generally
                                  developed by people who wish the programs to
                                  be outside of the GNU Public Licence scheme
   -[no]embassy        boolean    [Y] If you use this option then EMBASSY
                                  program documentation will be searched. If
                                  this option is set to be false, then only
                                  the EMBOSS programs will be searched (if the
                                  -emboss option is true). EMBASSY programs
                                  are not strictly part of EMBOSS, but use the
                                  same code libraries and share the same look
                                  and feel, but are generally developed by
                                  people who wish the programs to be outside
                                  of the GNU Public Licence scheme
   -showembassy        string     If you use this option then this EMBASSY
                                  package program documentation will be
                                  searched. EMBASSY programs are not strictly
                                  part of EMBOSS, but use the same code
                                  libraries and share the same look and feel,
                                  but are generally developed by people who
                                  wish the programs to be outside of the GNU
                                  Public Licence scheme (Any string is
                                  accepted)
   -colon              boolean    [N] The groups that EMBOSS applications
                                  belong to up to two levels, for example the
                                  primary group 'ALIGNMENT' has several
                                  sub-groups, or second-level groups, e.g.:
                                  CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL,
                                  LOCAL, MULTIPLE. To aid programs that parse
                                  the output of wossname that require the
                                  names of these subgroups, a colon ':' will
                                  be placed between the first and second level
                                  of the group name if this option is true.
                                  Note: This does not apply if the group names
                                  have been exploded with the 'explode'
                                  option.
   -gui                boolean    [N] This option is intended to help those
                                  who are designing Graphical User Interfaces
                                  to the EMBOSS applications. Some EMBOSS
                                  programs are inappropriate for running in a
                                  GUI, these include other menu programs and
                                  interactive editors. This option allows you
                                  to only report those programs that can be
                                  run from a GUI

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         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

Input file format

   wossname reads the brief descriptions and the program groups from the
   ACD files. (ACD files control the parameters that the programs expect
   - don't worry about them unless you are writing EMBOSS programs).

   The format of ACD files is documented elsewhere.

Output file format

   The results are written out as a simple list preceded by the group
   that the programs belong to or the word that is being searched for.

  Output files for usage example 5

  File: wossname.html



ACD

 Program name Description


  acdc  ACD compiler


  acdpretty  ACD pretty
   printing utility

  acdtable  Creates an HTML table from
   an ACD file

  acdtrace  ACD compiler on-screen
   trace

  acdvalid
    ACD file validation


ALIGNMENT CONSENSUS

 Program name Description


  cons  Creates a consensus
   from multiple alignments

  megamerger  Merge two large
   overlapping nucleic acid sequences

  merger  Merge two overlapping
   sequences


ALIGNMENT DIFFERENCES
  [Part of this file has been deleted
   for brevity]
 Program name Description


    dbiblast  Index a BLAST
   database

  dbifasta
    Database indexing for fasta file databases

  dbiflat  Index a flat file
   database

  dbigcg
    Index a GCG formatted database

  dbxfasta  Database b+tree indexing
   for fasta file databases

  dbxflat  Database b+tree indexing for
   flat file databases

  dbxgcg  Database b+tree indexing for
   GCG formatted databases


UTILS MISC

 Program name Description


  embossdata  Finds or
   fetches data files read by EMBOSS programs

  embossversion  Writes the
   current EMBOSS version number


   If the -html, -prelink and -postlink qualifiers are specified, then
   the output will be wrapped in HTML tags, ready for inclusion in a Web
   page. Note that tags such as

   , , and are not output by this program as the list of programs is
   expected to form only part of the contents of a web page - the rest of
   the web page must be supplied by the user. Data files As noted above,
   the program ACD files are searched. The average user will not need to
   worry about this. Notes If a program's ACD file does not assign the
   program to a group, it will be automatically assigned to the group
   'ASSORTED'. A program can belong to more than one group. The name of
   this program comes from its use as a favorite word of the author Terry
   Pratchett. It is used especially by the characters of the parrot in
   Eric and the dog Gaspode in Moving Pictures and Men at Arms.
   References None. Warnings None. Diagnostic Error Messages None. Exit
   status It always exits with status 0 Known bugs None. See also Program
   name Description infoalign Information on a multiple sequence
   alignment infoseq Displays some simple information about sequences
   seealso Finds programs sharing group names showdb Displays information
   on the currently available databases textsearch Search sequence
   documentation. Slow, use SRS and Entrez! tfm Displays a program's help
   documentation manual whichdb Search all databases for an entry
   Author(s) Gary Williams (gwilliam