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seealso |
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seealso takes the name of an EMBOSS or EMBASSY program and returns a list of applications in the same functional group. Application names and short descriptions are listed. Optionally, the output is written to an HTML table.
% seealso Finds programs with similar function to a specified program Program to search for: matcher SEE ALSO domainalign Generate alignments (DAF file) for nodes in a DCF file domainrep Reorder DCF file to identify representative structures oalistat Statistics for multiple alignment files seqalign Extend alignments (DAF file) with sequences (DHF file) seqmatchall All-against-all word comparison of a sequence set supermatcher Calculate approximate local pair-wise alignments of larger sequences water Smith-Waterman local alignment of sequences wordfinder Match large sequences against one or more other sequences wordmatch Finds regions of identity (exact matches) of two sequences |
Finds programs with similar function to a specified program
Version: EMBOSS:6.4.0.0
Standard (Mandatory) qualifiers:
[-search] string Enter the name of an EMBOSS program (Any
string of at least 1 characters)
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'.
Using expanded group names will find many
more programs which share at least some of
the expanded names than using the
non-exploded names and so you will get more
programs reported as sharing a similar
function than you will if you specify that
you wish to use non-exploded names
-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
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)
-colon boolean [N] The groups that EMBOSS applications
belong to have 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 seealso 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.
Associated qualifiers:
"-outfile" associated qualifiers
-odirectory string Output directory
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 | ||||
| [-search] (Parameter 1) |
string | Enter the name of an EMBOSS program | Any string of at least 1 characters | Required |
| Additional (Optional) qualifiers | ||||
| -explode | boolean | 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'. Using expanded group names will find many more programs which share at least some of the expanded names than using the non-exploded names and so you will get more programs reported as sharing a similar function than you will if you specify that you wish to use non-exploded names | Boolean value Yes/No | No |
| -outfile | outfile | Output file name | Output file | stdout |
| -html | toggle | If you are sending the output to a file, this will format it for displaying as a table in a WWW document. | Toggle value Yes/No | No |
| -groups | boolean | If you use this option, then only the group names will output to the file | Boolean value Yes/No | No |
| Advanced (Unprompted) qualifiers | ||||
| -[no]emboss | boolean | 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 | Boolean value Yes/No | Yes |
| -[no]embassy | boolean | 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 | Boolean value Yes/No | Yes |
| -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 | |
| -colon | boolean | The groups that EMBOSS applications belong to have 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 seealso 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. | Boolean value Yes/No | No |
| Associated qualifiers | ||||
| "-outfile" associated outfile qualifiers | ||||
| -odirectory | string | Output directory | 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 |
The result is header line 'SEE ALSO' then a simple list of program names followed by the one-line description of the program.
If the '-html' qualifier is used, then the result is an HTML-formatted table, lacking the HTML document structures such as <HTML>, <BODY>, </BODY>, </HTML> which the user is expected to provide as the table will usually be included in the middle of a larger HTML document.
The functional group of a program is set in its ACD file; this is an EMBOSS system file which specifies the application command-line interface such as required parameters, help on the parameters, one-line description of the program and so on. Normally the names of the groups are fairly specific. For example "NUCLEIC COMPOSITION" is a small group of applications for nucleotide sequence composition analysis.
The -explode qualifier will increase the number of groups that the program retrieves by splitting the group name at selected points to produce such groups as: "NUCLEIC", "NUCLEIC COMPOSITION" and "COMPOSITION". All programs with the exploded group names which also include "NUCLEIC" and "COMPOSITION" will now be reported. The result of this qualifier is thus a report of a larger number of programs with a more tenuous link to the specified program.
The groups that the program belongs to can be output by using the -groups qualifier.
The (optional) HTML-formatted table output lacks the HTML document structures such as ,
, , . It is expected the table will be included in the middle of a larger HTML document.FATAL ERROR: No application specified.is output if a non-existent program name is specified.
| Program name | Description |
|---|---|
| tfm | Displays full documentation for an application |
| wossdata | Finds programs by EDAM data |
| wossinput | Finds programs by EDAM input data |
| wossname | Finds programs by keywords in their short description |
| wossoperation | Finds programs by EDAM operation |
| wossoutput | Finds programs by EDAM output data |
| wossparam | Finds programs by EDAM parameter |
| wosstopic | Finds programs by EDAM topic |
Please report all bugs to the EMBOSS bug team (emboss-bug © emboss.open-bio.org) not to the original author.