DNA sequence recombination
This program cuts and recombines fragments from the same sequence
or different sequences and/or put some inserts.
The sequences are indexed in the order given
(the first sequence is numbered as 1, second as 2, and so on).
Each fragment is specified one per line
in the format of [r]seqnum:[start]-[end], such as
r1:650-970
2:500-765
s:GAATTC
r1:2900-100
3:3400-
The number before the colon specifies the index number of the sequence
from which the specified fragment is to be cut out.
If the optional leading 'r' is given, the orientation of the fragment,
after being cut out, is reversed before being combined with other fragments.
The number pairs, separated by '-', specify the start and end
locations of the fragment in the sequences to be cut.
If the number at the left of '-' is omitted, 1 is assumed.
If the number at the right is omitted,
the end of the sequence is assumed.
If the first number of a pair is bigger than the second number,
the fragment specified by those two numbers is taken as spanning
over the origin.
The sequence specified with "s:" is directly inserted into the final output.
The fragments and insert sequences are combined in the given order.
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