EMBOSS: extractseq

| ## EMBOSS: extractseq

# Program extractseq

## Function

Extract regions from a sequence

## Description

extractseq 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.

extractseq reads in a sequence and a set of regions of that sequence as specified by pairs of start and end positions (either on the command-line or contained in a file) and writes out the specified regions of the input sequence in the order in which they have been specified. Thus, if the sequence "AAAGGGTTT" has been input and the regions: "7-9, 3-4" have been specified, then the output sequence will be: "TTTAG".

## 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
       -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
      [-outseq]            seqoutall  Output sequence(s) USA

       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)
       General qualifiers:
      -help                bool       report command line options. More
                                      information on associated and general
                                      qualifiers can be found with -help -verbose

Mandatory qualifiers | Allowed values | Default
--- | --- | ---
[-sequence] (Parameter 1) | Sequence database USA | Readable sequence(s) | Required
-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
[-outseq] (Parameter 2) | Output sequence(s) USA | Writeable sequence(s) | <sequence>.format
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:

- Comment lines start with '#' in the first column.
- Comment lines and blank lines are ignored.
- The line may start with white-space.
- There are two positive (integer) numbers per line separated by one or more space or TAB characters.
- The second number must be greater or equal to the first number.
- There can be optional text after the two numbers to annotate the line.
- White-space before or after the text is removed.

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.

For example, the coding regions of em:hsfau1 are joined as:

    % extractseq em:hsfau1 -reg "782..856,951..1095,1557..1612,1787..1912" stdout

    >HSFAU X65923 H.sapiens fau mRNA
    atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg
    gtcgcccagatcaaggctcatgtagcctcactggagggcattgccccggaagatcaagtc
    gtgctcctggcaggcgcgcccctggaggatgaggccactctgggccagtgcggggtggag
    gccctgactaccctggaagtagcaggccgcatgcttggaggtaaagttcatggttccctg
    gcccgtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaagaagaag
    aagaagacaggtcgggctaagcggcggatgcagtacaaccggcgctttgtcaacgttgtg
    cccacctttggcaagaagaagggccccaatgccaactcttaa

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"

To output each of the exons in em:hsfau1 to a separate entry:

    % extractseq em:hsfau1 -reg "782..856,951..1095,1557..1612,1787..1912" stdout -separate

    >HSFAU1_782_856 H.sapiens fau 1 gene
    atgcagctctttgtccgcgcccaggagctacacaccttcgaggtgaccggccaggaaacg
    gtcgcccagatcaag
    >HSFAU1_951_1095 H.sapiens fau 1 gene
    gctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgctcctggcaggc
    gcgcccctggaggatgaggccactctgggccagtgcggggtggaggccctgactaccctg
    gaagtagcaggccgcatgcttggag
    >HSFAU1_1557_1612 H.sapiens fau 1 gene
    gtaaagtccatggttccctggcccgtgctggaaaagtgagaggtcagactcctaag
    >HSFAU1_1787_1912 H.sapiens fau 1 gene
    gtggccaaacaggagaagaagaagaagaagacaggtcgggctaagcggcggatgcagtac
    aaccggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccccaatgccaac
    tcttaa

## Data files

None.

## Notes

None.

## References

None.

## Warnings

None.

## Diagnostic Error Messages

Several warning messages about malformed region specifications:

- Non-digit found in region ...
- Unpaired start of a region found in ...
- Non-digit found in region ...
- The start of a pair of region positions must be smaller than the end in ...

## Exit status

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

## Known bugs

None noted.

## See also

Program name | Description
--- | ---
biosed | Replace or delete sequence sections
cutseq | Removes a specified section from a sequence
degapseq | Removes gap characters from sequences
descseq | Alter the name or description of a sequence
entret | Reads and writes (returns) flatfile entries
extractfeat | Extract features from a sequence
listor | Writes a list file of the logical OR of two sets of sequences
maskfeat | Mask off features of a sequence
maskseq | Mask off regions of a sequence
newseq | Type in a short new sequence
noreturn | Removes carriage return from ASCII files
notseq | Excludes a set of sequences and writes out the remaining ones
nthseq | Writes one sequence from a multiple set of sequences
pasteseq | Insert one sequence into another
revseq | Reverse and complement a sequence
seqret | Reads and writes (returns) sequences
seqretsplit | Reads and writes (returns) sequences in individual files
splitter | Split a sequence into (overlapping) smaller sequences
swissparse | Retrieves sequences from swissprot using keyword search
trimest | Trim poly-A tails off EST sequences
trimseq | Trim ambiguous bits off the ends of sequences
union | Reads sequence fragments and builds one sequence
vectorstrip | Strips out DNA between a pair of vector sequences
yank | Reads a sequence range, appends the full USA to a list file

## Author(s)

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

## History

Written (2000) - Gary Williams

## Target users

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

## Comments