| Data type / Object |
Description |
Commandline (associated) Qualifiers |
| |
| Simple types |
| boolean |
Boolean parameters are simple switches. If they are entered on the
command line the value will be Y (True), if they are absent from the
command line the value will be the default value. The name can also be
prefixed by 'no' to force the value to be N (False). This is needed in
case the default value is Y (True). |
none |
| integer |
The integer data type can hold simple integer values. |
none |
| float |
Floating point number |
none |
| range |
Ranges of sequence positions. Originally defined as simple list of
paired numbers, ranges can now be specified in files with the range syntax
"@filename", for example:
# this is my set of ranges
12 23
4 5 this is like 12-23, but smaller
67 10348 interesting region
|
none |
| regexp |
Any regular expression pattern value |
none |
| string |
Any string (text) value. If the string contains spaces then it should be enclosed in ' '. |
none |
| Input |
| infile |
Input file (non-sequence file) This data type refers to files
that are to be used in the program and do usually not contain sequence
data. |
none |
| matrix |
Scoring matrix (integer) for alignments. Comparison matrix files are used by many programs. They are data
files read from the EMBOSS data search path, and are distributed in
the emboss/data directory. For preference, we use the matrix files
distributed with BLAST.
Integer matrices are usually faster and are preferred by most
applications. Floating point matrix files are also available if
needed, and an integer matrix file can of course also be read as
floating point.
|
none |
| matrixf |
Scoring matrix (floating point) for alignments. See matrix above. |
none |
| codon |
Codon usage table |
none |
| sequence |
USA containing a single sequence. |
-sformat
-sask: N
-sbegin: 0
-send: sequence length
-sreverse: N
-slower: N
-supper: N
-snucleotide: N
-sprotein: N
-sdbname
-sentry
-sopenfile
-ufo
-fformat
-fopenfile
|
| seqset |
Input sequence set of single sequences, that can be addressed one after another
(for example a set of sequences that will be used in an multiple
alignment). |
-sformat
-sask: N
-sbegin: 0
-send: sequence length
-sreverse: N
-slower: N
-supper: N
-snucleotide: N
-sprotein: N
-sdbname
-sentry
-sopenfile
-ufo
-fformat
-fopenfile
|
| seqall |
A set of single sequences, that can be used all at the same time
(for example a database of some sort that is to be used for a pattern
search). |
-sformat
-sask: N
-sbegin: 0
-send: sequence length
-sreverse: N
-slower: N
-supper: N
-sprotein
-snucleotide
-sopenfile
-sdbname
-sentry
-sopenfile
-ufo
-fformat
-fopenfile
|
| features |
Feature table UFO (Uniform Feature Object) This contains sequence annotation information. |
-fformat
-fopenfile
-fask
-fbegin
-fend
-freverse
|
| Selection lists |
| list/selection |
List of options of which one or more can be selected. |
none |
| Output |
| outfile |
Output file (non-sequence). See infile. |
none |
| seqout/seqoutset |
Output sequence set. See seqset. Seqout can be used for outputting either a single sequence or a set of sequences. |
-osformat
-osextension
-osname
-osdbname
-ossingle
-oufo
-offormat
-ofname
|
| seqoutall |
Output all sequences. |
-osformat
-osextension
-osname
-osdbname
-ossingle
-oufo
-offormat
-ofname
|
| featout |
Output feature table |
-offormat
-ofopenfile
-ofextension
-ofname
-ofsingle
|
| Graphics |
| graph |
Graphics output device or format. This takes graphical output of any general kind, including dotplots. |
-gprompt
-gtitle
-gsubtitle
-gxtitle
-gytitle
-grtitle
-gpages
-gsets
-goutfile
|
| xygraph |
2D plot output device for
graphical output as a simple XY plot with the sequence along the x axis. |
-gprompt
-gtitle
-gsubtitle
-gxtitle
-gytitle
-grtitle
-gpages
|
