EMBOSS: seqretfeat

Program seqretfeat

Function

Reads and writes (returns) a sequence and outputs the feature table for it

Description

Usage

Here is a sample session with seqretfeat.


% seqretfeat

Command line arguments

   Mandatory qualifiers: (none)
   Optional qualifiers: (none)
   Advanced qualifiers:
   -featignore         string     Comma delimited list of Features NOT to be
                                  output
   -featonlyallow      string     Comma delimited list of Features to be
                                  output,
                                  will have no effect if featignore is set
   -tagignore          string     Comma delimited list of Tags NOT to be
                                  output
   -tagonlyallow       string     Comma delimited list of Tags to be output,
                                  will have no effect if tagignore is set
   -sortbytype         bool       Sort output features by their type
   -sortbystart        bool       Sort output features by their start position

Mandatory qualifiers Allowed values Default

(none)

Optional qualifiers Allowed values Default

(none)

Advanced qualifiers Allowed values Default

-featignore Comma delimited list of Features NOT to be output Any string is accepted An empty string is accepted

-featonlyallow Comma delimited list of Features to be output, will have no effect if featignore is set Any string is accepted An empty string is accepted

-tagignore Comma delimited list of Tags NOT to be output Any string is accepted An empty string is accepted

-tagonlyallow Comma delimited list of Tags to be output, will have no effect if tagignore is set Any string is accepted An empty string is accepted

-sortbytype Sort output features by their type Yes/No No

-sortbystart Sort output features by their start position Yes/No No

Mandatory qualifiers	Allowed values	Default
(none)
Optional qualifiers	Allowed values	Default
(none)
Advanced qualifiers	Allowed values	Default
-featignore	Comma delimited list of Features NOT to be output	Any string is accepted	An empty string is accepted
-featonlyallow	Comma delimited list of Features to be output, will have no effect if featignore is set	Any string is accepted	An empty string is accepted
-tagignore	Comma delimited list of Tags NOT to be output	Any string is accepted	An empty string is accepted
-tagonlyallow	Comma delimited list of Tags to be output, will have no effect if tagignore is set	Any string is accepted	An empty string is accepted
-sortbytype	Sort output features by their type	Yes/No	No
-sortbystart	Sort output features by their start position	Yes/No	No

Input file format

Output file format

Data files

Notes

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

Author(s)

This application was written by Peter Rice (pmr@sanger.ac.uk) Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

History

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.