extractseq allows you to specify one or more regions of a sequence to extract subsequences from to build up a contiguous resulting sequence.

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'

Mandatory qualifiers:

[-sequence] (sequence)

Sequence 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, or 1,5,8,10,23,45,57,99.

[-outseq] (seqoutall)

Output sequence(s) USA.

Optional qualifiers:

-separate (boolean)

If this is set true, 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 underscore characters between the start and end positions of the range. For example, XYZ region 2 to 34 is written as: XYZ_2_34.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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