Man pages sections > man1 > extractseq

extractseq - Extract regions from a sequence

EXTRACTSEQ(1e) EMBOSS Manual for Debian EXTRACTSEQ(1e)

NAME

extractseq - Extract regions from a sequence

SYNOPSIS

extractseq -sequence sequence -regions range [-separate boolean] -outseq seqoutall
extractseq -help

DESCRIPTION

extractseq is a command line program from EMBOSS (“the European Molecular Biology Open Software Suite”). It is part of the "Edit" command group(s).

OPTIONS

Input section

-sequence sequence

Required section

-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 Default value: $(sequence.begin)-$(sequence.end)

Additional section

-separate boolean
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 Default value: N

Output section

-outseq seqoutall

BUGS

Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

SEE ALSO

extractseq is fully documented via the tfm(1) system.

AUTHOR

Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual page.
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself.
 
05/11/2012 EMBOSS 6.4.0