EMBOSS: extractseq


Program extractseq

Function

Extract regions from a sequence

Description

This allows you to specify one or more regions of a sequence to extract sub-sequences from to build up a contiguous resulting sequence.

This is modelled on the cell's process of splicing out exons from mRNA, but the program is generally applicable to any cutting and splicing or editing operation on a single sequence.

Usage

Extract the region from position 10 to 20.
% extractseq main.seq result.seq -regions '10-20'

Extract the regions 10 to 20, 30 to 45, 533 to 537

% extractseq main.seq result2.seq -regions '10-20, 30-45, 533-537'

Command line arguments

   Mandatory qualifiers:
  [-sequence]          seqall     Sequence database USA
  [-outseq]            seqoutall  Output sequence(s) USA
   -regions            range      Regions to extract.
                                  A set of regions is specified by a set of
                                  pairs of positions.
                                  The positions are integers.
                                  They are separated by any non-digit,
                                  non-alpha character.
                                  Examples of region specifications are:
                                  24-45, 56-78
                                  1:45, 67=99;765..888
                                  1,5,8,10,23,45,57,99

   Optional qualifiers:
   -separate           bool       If this is set true then each specified
                                  region is written out as a separate
                                  sequence. The name of the sequence is
                                  created from the name of the original
                                  sequence with the start and end positions of
                                  the range appended with underscore
                                  characters between them, eg: XYZ region 2 to
                                  34 is written as: XYZ_2_34

   Advanced qualifiers: (none)

Mandatory qualifiers Allowed values Default
[-sequence]
(Parameter 1)
Sequence database USA Readable sequence(s) Required
[-outseq]
(Parameter 2)
Output sequence(s) USA Writeable sequence(s) <sequence>.format
-regions Regions to extract. A set of regions is specified by a set of pairs of positions. The positions are integers. They are separated by any non-digit, non-alpha character. Examples of region specifications are: 24-45, 56-78 1:45, 67=99;765..888 1,5,8,10,23,45,57,99 Sequence range Whole sequence
Optional qualifiers Allowed values Default
-separate If this is set true then each specified region is written out as a separate sequence. The name of the sequence is created from the name of the original sequence with the start and end positions of the range appended with underscore characters between them, eg: XYZ region 2 to 34 is written as: XYZ_2_34 Yes/No No
Advanced qualifiers Allowed values Default
(none)

Input file format

Normal sequence.

You can specifiy a file of ranges to extract by giving the '-regions' qualifier the value '@' followed by the name of the file containing the ranges. (eg: '-regions @myfile').

The format of the range file is:

An example range file is:


# this is my set of ranges
12   23
 4   5       this is like 12-23, but smaller
67   10348   interesting region

Output file format

The output is a normal sequence file.

If the option '-separate' is used then each specified region is written to the output file as a separate sequence. The name of the sequence is created from the name of the original sequence with the start and end positions of the range appended with underscore characters between them,

For example: "XYZ region 2 to 34" is written as: "XYZ_2_34"

Data files

None.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

Several warning messages about malformed region specifications:

Exit status

It exits with status 0, unless a region is badly constructed.

Known bugs

None noted.

See also

Program nameDescription
cutseqRemoves a specified section from a sequence
descseqAlter the name or description of a sequence
maskfeatMask off features of a sequence
maskseqMask off regions of a sequence
megamergerMerge two large overlapping nucleic acid sequences
mergerMerge two overlapping nucleic acid sequences
newseqType in a short new sequence
noreturnRemoves carriage return from ASCII files
nthseqWrites one sequence from a multiple set of sequences
pasteseqInsert one sequence into another
revseqReverse and complement a sequence
splitterSplit a sequence into (overlapping) smaller sequences
trimseqTrim ambiguous bits off the ends of sequences
vectorstripStrips out DNA between a pair of vector sequences

Author(s)

This application was written by Gary Williams (gwilliam@hgmp.mrc.ac.uk)

History

Finished.

Target users

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

Comments