extractseq reads a sequence and writes sub-sequences from it to file. The set of regions to extract is specified on the command-line or in a file as pairs of start and end positions. The regions are written in the order in which they are 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. Optionally, each region may be written out as a separate sequence.
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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
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"
extractseq allows you to specify one or more regions of a sequence to extract sub-sequences from to build up a contiguous output 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.
Where the -regions option is used to specify output as separate sequences, 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. In such cases the output sequence foramt must be capable of supporting multiple sequences.